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galaxy-dist commit 1ebd342fb4eb: branch merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289244516 18000 # Node ID 1ebd342fb4eb29c095b19a960503402f75cbe944 # Parent d344c55b4f81f273d712c397d648fbaf308a9beb # Parent 3ea6ee14a8b71cd7ac48da98a6ecdb50b9067040 branch merge

1 0

galaxy-dist commit 43c1f36a8e4e: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289249727 18000 # Node ID 43c1f36a8e4e3f9aa62dc9bc144e54b8312364bf # Parent 2f02897723c2f3c1d0d7be8c14f4c664409e1c59 # Parent eee0e1d344d21de7fb079fcccc3df8e251d1e025 merge --- a/test-data/tophat_out1.sam +++ /dev/null @@ -1,179 +0,0 @@ -test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_104_274_1c 73 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 NH:i:1 -test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_111_268_d 73 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_11_190_1a 99 test_chromosome 61 255 75M = 166 0 GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_128_252_36 137 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_150_290_0 73 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_151_286_e 137 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_151_297_1d 137 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_16_194_10 163 test_chromosome 66 255 75M = 170 0 GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_21_208_24 163 test_chromosome 71 255 75M = 184 0 GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_22_173_62 99 test_chromosome 72 255 75M = 149 0 AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_23_186_42 163 test_chromosome 73 255 75M = 162 0 GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_26_189_30 163 test_chromosome 76 255 75M = 165 0 GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_28_188_11 99 test_chromosome 78 255 75M = 164 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_28_206_1f 73 test_chromosome 78 255 75M * 0 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_30_231_3c 161 test_chromosome 80 255 75M = 207 0 GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_33_189_4a 73 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_33_223_4e 73 test_chromosome 83 255 75M * 0 0 ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_36_146_27 163 test_chromosome 86 255 75M = 122 0 GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_36_218_12 99 test_chromosome 86 255 75M = 194 0 GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 99 test_chromosome 88 255 75M = 175 0 GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_39_219_5c 99 test_chromosome 89 255 75M = 195 0 CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_41_236_55 97 test_chromosome 91 255 75M = 212 0 AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_42_209_25 99 test_chromosome 92 255 75M = 185 0 GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_44_193_3f 99 test_chromosome 94 255 75M = 169 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_197_35 99 test_chromosome 94 255 75M = 173 0 ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_225_1e 163 test_chromosome 94 255 75M = 201 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_46_195_17 137 test_chromosome 96 255 75M * 0 0 GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_46_232_2f 99 test_chromosome 96 255 75M = 208 0 GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_207_39 73 test_chromosome 98 255 75M * 0 0 GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_48_249_20 161 test_chromosome 98 255 75M = 225 0 GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 163 test_chromosome 100 255 75M = 200 0 CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_51_194_47 163 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_51_194_49 99 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_51_237_a 99 test_chromosome 101 255 75M = 213 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_51_248_14 97 test_chromosome 101 255 75M = 224 0 ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_52_261_1b 97 test_chromosome 102 255 75M = 237 0 CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_53_212_19 99 test_chromosome 103 255 75M = 188 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_53_272_5a 161 test_chromosome 103 255 75M = 248 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_56_183_56 99 test_chromosome 106 255 75M = 159 0 GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_57_231_8 99 test_chromosome 107 255 75M = 207 0 GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 163 test_chromosome 108 255 75M = 194 0 GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_58_220_3d 163 test_chromosome 108 255 75M = 196 0 GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_58_234_7 163 test_chromosome 108 255 75M = 210 0 GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_63_229_4c 163 test_chromosome 113 255 75M = 205 0 ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 99 test_chromosome 115 255 75M = 214 0 GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_69_229_23 163 test_chromosome 119 255 75M = 205 0 AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 163 test_chromosome 122 255 75M = 234 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_73_240_34 99 test_chromosome 123 255 75M = 216 0 CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_259_5e 99 test_chromosome 123 255 75M = 235 0 CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_204_54 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_235_21 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_75_277_3b 97 test_chromosome 125 255 75M = 353 0 ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_77_256_2c 73 test_chromosome 127 255 75M * 0 0 GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_78_276_4b 97 test_chromosome 128 255 75M = 352 0 GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_79_256_31 137 test_chromosome 129 255 75M * 0 0 ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_81_228_3a 163 test_chromosome 131 255 75M = 204 0 GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_81_245_4d 163 test_chromosome 131 255 75M = 221 0 GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_82_255_2 137 test_chromosome 132 255 75M * 0 0 GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_82_271_58 99 test_chromosome 132 255 75M = 247 0 GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_85_268_53 99 test_chromosome 135 255 75M = 244 0 TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_275_38 137 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_87_250_57 163 test_chromosome 137 255 75M = 226 0 AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_87_279_5f 161 test_chromosome 137 255 75M = 355 0 AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_88_257_50 137 test_chromosome 138 255 75M * 0 0 GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_230_b 163 test_chromosome 139 255 75M = 206 0 AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_89_245_15 99 test_chromosome 139 255 75M = 221 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_267_32 163 test_chromosome 139 255 75M = 243 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_91_256_41 73 test_chromosome 141 255 75M * 0 0 CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_92_250_44 99 test_chromosome 142 255 75M = 226 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_92_266_43 99 test_chromosome 142 255 75M = 242 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_94_291_40 137 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_96_238_3 163 test_chromosome 146 255 75M = 214 0 GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_97_275_26 97 test_chromosome 147 255 75M = 351 0 ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 83 test_chromosome 155 255 75M = 59 0 ACTGGACCATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 --- a/test-data/tophat_out2.wig +++ /dev/null @@ -1,175 +0,0 @@ -track type=bedGraph name="TopHat - read coverage" -test_chromosome 0 52 0 -test_chromosome 52 53 1 -test_chromosome 53 54 2 -test_chromosome 54 55 3 -test_chromosome 55 57 4 -test_chromosome 57 58 6 -test_chromosome 58 60 7 -test_chromosome 60 65 8 -test_chromosome 65 70 9 -test_chromosome 70 71 10 -test_chromosome 71 72 11 -test_chromosome 72 75 12 -test_chromosome 75 77 13 -test_chromosome 77 79 15 -test_chromosome 79 82 16 -test_chromosome 82 85 17 -test_chromosome 85 87 19 -test_chromosome 87 88 20 -test_chromosome 88 90 21 -test_chromosome 90 91 22 -test_chromosome 91 93 23 -test_chromosome 93 95 26 -test_chromosome 95 97 28 -test_chromosome 97 99 30 -test_chromosome 99 100 31 -test_chromosome 100 101 35 -test_chromosome 101 102 36 -test_chromosome 102 105 38 -test_chromosome 105 106 39 -test_chromosome 106 107 40 -test_chromosome 107 112 43 -test_chromosome 112 114 44 -test_chromosome 114 118 45 -test_chromosome 118 121 46 -test_chromosome 121 122 48 -test_chromosome 122 124 50 -test_chromosome 124 126 53 -test_chromosome 126 129 54 -test_chromosome 129 130 53 -test_chromosome 130 131 55 -test_chromosome 131 132 57 -test_chromosome 132 133 55 -test_chromosome 133 134 54 -test_chromosome 134 135 55 -test_chromosome 135 136 54 -test_chromosome 136 137 56 -test_chromosome 137 138 57 -test_chromosome 138 141 60 -test_chromosome 141 147 62 -test_chromosome 147 148 61 -test_chromosome 148 150 62 -test_chromosome 150 152 61 -test_chromosome 152 153 60 -test_chromosome 153 154 61 -test_chromosome 154 155 63 -test_chromosome 155 156 64 -test_chromosome 156 158 65 -test_chromosome 158 159 66 -test_chromosome 159 160 68 -test_chromosome 160 161 67 -test_chromosome 161 163 68 -test_chromosome 163 164 69 -test_chromosome 164 165 71 -test_chromosome 165 167 73 -test_chromosome 167 168 74 -test_chromosome 168 169 72 -test_chromosome 169 170 75 -test_chromosome 170 171 73 -test_chromosome 171 172 74 -test_chromosome 172 174 75 -test_chromosome 174 175 77 -test_chromosome 175 176 74 -test_chromosome 176 177 73 -test_chromosome 177 181 71 -test_chromosome 181 182 70 -test_chromosome 182 183 67 -test_chromosome 183 184 68 -test_chromosome 184 189 69 -test_chromosome 189 193 68 -test_chromosome 193 194 69 -test_chromosome 194 195 71 -test_chromosome 195 196 72 -test_chromosome 196 197 70 -test_chromosome 197 199 68 -test_chromosome 199 200 66 -test_chromosome 200 201 67 -test_chromosome 201 202 66 -test_chromosome 202 204 65 -test_chromosome 204 205 67 -test_chromosome 205 207 65 -test_chromosome 207 211 66 -test_chromosome 211 213 65 -test_chromosome 213 216 64 -test_chromosome 216 220 62 -test_chromosome 220 224 63 -test_chromosome 224 225 64 -test_chromosome 225 228 66 -test_chromosome 228 229 65 -test_chromosome 229 230 62 -test_chromosome 230 231 61 -test_chromosome 231 232 60 -test_chromosome 232 234 59 -test_chromosome 234 237 58 -test_chromosome 237 238 57 -test_chromosome 238 239 55 -test_chromosome 239 240 53 -test_chromosome 240 241 50 -test_chromosome 241 242 51 -test_chromosome 242 243 52 -test_chromosome 243 244 53 -test_chromosome 244 246 50 -test_chromosome 246 247 52 -test_chromosome 247 249 50 -test_chromosome 249 250 47 -test_chromosome 250 349 0 -test_chromosome 349 350 1 -test_chromosome 350 351 49 -test_chromosome 351 352 51 -test_chromosome 352 353 53 -test_chromosome 353 354 54 -test_chromosome 354 357 55 -test_chromosome 357 358 56 -test_chromosome 358 361 55 -test_chromosome 361 362 57 -test_chromosome 362 365 56 -test_chromosome 365 366 57 -test_chromosome 366 368 58 -test_chromosome 368 369 57 -test_chromosome 369 372 56 -test_chromosome 372 375 59 -test_chromosome 375 378 60 -test_chromosome 378 379 59 -test_chromosome 379 380 57 -test_chromosome 380 381 56 -test_chromosome 381 382 54 -test_chromosome 382 384 53 -test_chromosome 384 386 52 -test_chromosome 386 387 51 -test_chromosome 387 388 50 -test_chromosome 388 390 48 -test_chromosome 390 395 47 -test_chromosome 395 396 45 -test_chromosome 396 398 44 -test_chromosome 398 399 43 -test_chromosome 399 400 42 -test_chromosome 400 402 1 -test_chromosome 402 500 0 -test_chromosome 500 508 39 -test_chromosome 508 509 38 -test_chromosome 509 510 37 -test_chromosome 510 511 36 -test_chromosome 511 516 35 -test_chromosome 516 517 33 -test_chromosome 517 518 31 -test_chromosome 518 521 29 -test_chromosome 521 522 26 -test_chromosome 522 524 25 -test_chromosome 524 525 24 -test_chromosome 525 526 22 -test_chromosome 526 527 20 -test_chromosome 527 528 18 -test_chromosome 528 529 17 -test_chromosome 529 530 16 -test_chromosome 530 532 15 -test_chromosome 532 534 14 -test_chromosome 534 536 13 -test_chromosome 536 540 11 -test_chromosome 540 541 10 -test_chromosome 541 543 9 -test_chromosome 543 544 8 -test_chromosome 544 545 7 -test_chromosome 545 547 6 -test_chromosome 547 549 3 -test_chromosome 549 549 2 --- a/test-data/tophat_out3.bed +++ /dev/null @@ -1,3 +0,0 @@ -track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151

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galaxy-dist commit 2c2baca25528: rgHaploView.py reorganized to make a little less ugly and easier to maintain
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289249136 18000 # Node ID 2c2baca255289cd48ecb806cfb0ea6468d489bde # Parent eee0e1d344d21de7fb079fcccc3df8e251d1e025 rgHaploView.py reorganized to make a little less ugly and easier to maintain --- a/tools/rgenetics/rgHaploView.py +++ b/tools/rgenetics/rgHaploView.py @@ -33,11 +33,466 @@ javabin = 'java' atrandic = {'A':'1','C':'2','G':'3','T':'4','N':'0','-':'0','1':'1','2':'2','3':'3','4':'4','0':'0'} class NullDevice: - """ """ + """ a dev/null for ignoring output + """ def write(self, s): pass -def ld(): +class ldPlot: + + def __init__(self, argv=[]): + """ + setup + """ + self.args=argv + self.parseArgs(argv=self.args) + self.setupRegions() + + def parseArgs(self,argv=[]): + """ + """ + ts = '%s%s' % (string.punctuation,string.whitespace) + ptran = string.maketrans(ts,'_'*len(ts)) + ### Figure out what genomic region we are interested in + self.region = argv[1] + self.orslist = argv[2].replace('X',' ').lower() # galaxy replaces newlines with XX - go figure + self.title = argv[3].translate(ptran) + # for outputs + self.outfile = argv[4] + self.logfn = 'Log_%s.txt' % (self.title) + self.histextra = argv[5] + self.base_name = argv[6] + self.pedFileBase = os.path.join(self.histextra,self.base_name) + print 'pedfilebase=%s' % self.pedFileBase + self.minMaf=argv[7] + if self.minMaf: + try: + self.minMaf = float(self.minMaf) + except: + self.minMaf = 0.0 + self.maxDist=argv[8] or None + self.ldType=argv[9] or 'RSQ' + self.hiRes = (argv[10].lower() == 'hi') + self.memSize= argv[11] or '1000' + self.memSize = int(self.memSize) + self.outfpath = argv[12] + self.infotrack = False # note that otherwise this breaks haploview in headless mode + #infotrack = argv[13] == 'info' + # this fails in headless mode as at april 2010 with haploview 4.2 + self.tagr2 = argv[14] or '0.8' + hmpanels = argv[15] # eg "['CEU','YRI']" + if hmpanels: + hmpanels = hmpanels.replace('[','') + hmpanels = hmpanels.replace(']','') + hmpanels = hmpanels.replace("'",'') + hmpanels = hmpanels.split(',') + self.hmpanels = hmpanels + self.hvbin = argv[16] # added rml june 2008 + self.bindir = os.path.split(self.hvbin)[0] + # jan 2010 - always assume utes are on path to avoid platform problems + self.pdfjoin = 'pdfjoin' # os.path.join(bindir,'pdfjoin') + self.pdfnup = 'pdfnup' # os.path.join(bindir,'pdfnup') + self.mogrify = 'mogrify' # os.path.join(bindir,'mogrify') + self.convert = 'convert' # os.path.join(bindir,'convert') + self.log_file = os.path.join(self.outfpath,self.logfn) + self.MAP_FILE = '%s.map' % self.pedFileBase + self.DATA_FILE = '%s.ped' % self.pedFileBase + try: + os.makedirs(self.outfpath) + s = '## made new path %s\n' % self.outfpath + except: + pass + self.lf = file(self.log_file,'w') + s = 'PATH=%s\n' % os.environ.get('PATH','?') + self.lf.write(s) + + def setupRegions(self): + """ + """ + chromosome = '' + spos = epos = -9 + rslist = [] + rsdict = {} + + if self.region > '': + useRs = [] + useRsdict={} + try: # TODO make a regexp? + c,rest = self.region.split(':') + chromosome = c.replace('chr','') + rest = rest.replace(',','') # remove commas + spos,epos = rest.split('-') + spos = int(spos) + epos = int(epos) + s = '## %s parsing chrom %s from %d to %d\n' % (progname,chromosome,spos,epos) + self.lf.write(s) + self.lf.write('\n') + print >> sys.stdout, s + except: + s = '##! %s unable to parse region %s - MUST look like "chr8:10,000-100,000\n' % (progname,self.region) + print >> sys.stdout, s + self.lf.write(s) + self.lf.write('\n') + self.lf.close() + sys.exit(1) + else: + useRs = self.orslist.split() # galaxy replaces newlines with XX - go figure + useRsdict = dict(zip(useRs,useRs)) + self.useTemp = False + try: + dfile = open(self.DATA_FILE, 'r') + except: # bad input file name? + s = '##! RGeno unable to open file %s\n' % (self.DATA_FILE) + self.lf.write(s) + self.lf.write('\n') + self.lf.close() + print >> sys.stdout, s + raise + sys.exit(1) + try: + mfile = open(self.MAP_FILE, 'r') + except: # bad input file name? + s = '##! RGeno unable to open file %s' % (self.MAP_FILE) + lf.write(s) + lf.write('\n') + lf.close() + print >> sys.stdout, s + raise + sys.exit(1) + if len(useRs) > 0 or spos <> -9 : # subset region + self.useTemp = True + ### Figure out which markers are in this region + markers = [] + snpcols = {} + chroms = {} + minpos = 2**32 + maxpos = 0 + for lnum,row in enumerate(mfile): + line = row.strip() + if not line: continue + chrom, snp, genpos, abspos = line.split() + try: + ic = int(chrom) + except: + ic = None + if ic and ic <= 23: + try: + abspos = int(abspos) + if abspos > maxpos: + maxpos = abspos + if abspos < minpos: + minpos = abspos + except: + abspos = epos + 999999999 # so next test fails + if useRsdict.get(snp,None) or (spos <> -9 and chrom == chromosome and (spos <= abspos <= epos)): + if chromosome == '': + chromosome = chrom + chroms.setdefault(chrom,chrom) + markers.append((chrom,abspos,snp)) # decorate for sort into genomic + snpcols[snp] = lnum # so we know which col to find genos for this marker + markers.sort() + rslist = [x[2] for x in markers] # drop decoration + rsdict = dict(zip(rslist,rslist)) + if len(rslist) == 0: + s = '##! %s found no rs numbers in %s' % (progname,argv[1:3]) + self.lf.write(s) + self.lf.write('\n') + self.lf.close() + print >> sys.stdout, s + sys.exit(1) + if spos == -9: + spos = minpos + epos = maxpos + s = '## %s looking for %d rs (%s)' % (progname,len(rslist),rslist[:5]) + self.lf.write(s) + print >> sys.stdout, s + wewant = [(6+(2*snpcols[x])) for x in rslist] # + # column indices of first geno of each marker pair to get the markers into genomic + ### ... and then parse the rest of the ped file to pull out + ### the genotypes for all subjects for those markers + # /usr/local/galaxy/data/rg/1/lped/ + self.tempMapName = os.path.join(self.outfpath,'%s.info' % self.title) + self.tempMap = file(self.tempMapName,'w') + self.tempPedName = os.path.join(self.outfpath,'%s.ped' % self.title) + self.tempPed = file(self.tempPedName,'w') + self.pngpath = '%s.LD.PNG' % self.tempPedName + map = ['%s\t%s' % (x[2],x[1]) for x in markers] # snp,abspos in genomic order for haploview + self.tempMap.write('%s\n' % '\n'.join(map)) + self.tempMap.close() + nrows = 0 + for line in dfile: + line = line.strip() + if not line: + continue + fields = line.split() + preamble = fields[:6] + g = ['%s %s' % (fields[snpcol], fields[snpcol+1]) for snpcol in wewant] + g = ' '.join(g) + g = g.split() # we'll get there + g = [atrandic.get(x,'0') for x in g] # numeric alleles... + self.tempPed.write('%s %s\n' % (' '.join(preamble), ' '.join(g))) + nrows += 1 + self.tempPed.close() + s = '## %s: wrote %d markers, %d subjects for region %s\n' % (progname,len(rslist),nrows,self.region) + self.lf.write(s) + self.lf.write('\n') + print >> sys.stdout,s + else: # even if using all, must set up haploview info file instead of map + markers = [] + chroms = {} + spos = sys.maxint + epos = -spos + for lnum,row in enumerate(mfile): + line = row.strip() + if not line: continue + chrom, snp, genpos, abspos = line.split() + try: + ic = int(chrom) + except: + ic = None + if ic and ic <= 23: + if chromosome == '': + chromosome = chrom + chroms.setdefault(chrom,chrom) + try: + p = int(abspos) + if p < spos and p <> 0: + spos = p + if p > epos and p <> 0: + epos = p + except: + pass + markers.append('%s %s' % (snp,abspos)) # no sort - pass + # now have spos and epos for hapmap if hmpanels + self.tempMapName = os.path.join(self.outfpath,'%s.info' % self.title) + self.tempMap = file(self.tempMapName,'w') + self.tempMap.write('\n'.join(markers)) + self.tempMap.close() + self.tempPedName = os.path.join(self.outfpath,'%s.ped' % self.title) + try: # will fail on winblows! + os.symlink(self.DATA_FILE,self.tempPedName) + except: + shutil.copy(self.DATA_FILE,self.tempPedName) # wasteful but.. + self.nchroms = len(chroms) # if > 1 can't really do this safely + dfile.close() + mfile.close() + self.spos = spos + self.epos = epos + self.chromosome = chromosome + if self.nchroms > 1: + s = '## warning - multiple chromosomes found in your map file - %s\n' % ','.join(chroms.keys()) + self.lf.write(s) + print >> sys.stdout,s + sys.exit(1) + + def doPlots(self): + """ + """ + DATA_FILE = self.tempPedName # for haploview + INFO_FILE = self.tempMapName + fblog,blog = tempfile.mkstemp() + ste = open(blog,'w') # to catch the blather + # if no need to rewrite - set up names for haploview call + vcl = [javabin,'-jar',self.hvbin,'-n','-memory','%d' % self.memSize,'-pairwiseTagging', + '-pedfile',DATA_FILE,'-info',INFO_FILE,'-tagrsqcounts', + '-tagrsqcutoff',self.tagr2, '-ldcolorscheme',self.ldType] + if self.minMaf: + vcl += ['-minMaf','%f' % self.minMaf] + if self.maxDist: + vcl += ['-maxDistance',self.maxDist] + if self.hiRes: + vcl.append('-png') + else: + vcl.append('-compressedpng') + if self.nchroms == 1: + vcl += ['-chromosome',self.chromosome] + if self.infotrack: + vcl.append('-infoTrack') + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=ste,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + vcl = [self.mogrify, '-resize 800x400!', '*.PNG'] + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + inpng = '%s.LD.PNG' % DATA_FILE # stupid but necessary - can't control haploview name mangle + inpng = inpng.replace(' ','') + inpng = os.path.split(inpng)[-1] + tmppng = '%s.tmp.png' % self.title + tmppng = tmppng.replace(' ','') + outpng = '1_%s.png' % self.title + outpng = outpng.replace(' ','') + outpng = os.path.split(outpng)[-1] + vcl = [self.convert, '-resize 800x400!', inpng, tmppng] + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + s = "text 10,300 '%s'" % self.title[:40] + vcl = [self.convert, '-pointsize 25','-fill maroon', + '-draw "%s"' % s, tmppng, outpng] + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + try: + os.remove(os.path.join(self.outfpath,tmppng)) + except: + pass # label all the plots then delete all the .PNG files before munging + fnum=1 + if self.hmpanels: + sp = '%d' % (self.spos/1000.) # hapmap wants kb + ep = '%d' % (self.epos/1000.) + for panel in self.hmpanels: + if panel > '' and panel.lower() <> 'none': # in case someone checks that option too :) + ptran = panel.strip() + ptran = ptran.replace('+','_') + fnum += 1 # preserve an order or else we get sorted + vcl = [javabin,'-jar',self.hvbin,'-n','-memory','%d' % self.memSize, + '-chromosome',self.chromosome, '-panel',panel.strip(), + '-hapmapDownload','-startpos',sp,'-endpos',ep, + '-ldcolorscheme',self.ldType] + if self.minMaf: + vcl += ['-minMaf','%f' % self.minMaf] + if self.maxDist: + vcl += ['-maxDistance',self.maxDist] + if self.hiRes: + vcl.append('-png') + else: + vcl.append('-compressedpng') + if self.infotrack: + vcl.append('-infoTrack') + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=ste,stdout=self.lf) + retval = p.wait() + inpng = 'Chromosome%s%s.LD.PNG' % (self.chromosome,panel) + inpng = inpng.replace(' ','') # mysterious spaces! + outpng = '%d_HapMap_%s_%s.png' % (fnum,ptran,self.chromosome) + # hack for stupid chb+jpt + outpng = outpng.replace(' ','') + tmppng = '%s.tmp.png' % self.title + tmppng = tmppng.replace(' ','') + outpng = os.path.split(outpng)[-1] + vcl = [self.convert, '-resize 800x400!', inpng, tmppng] + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + s = "text 10,300 'HapMap %s'" % ptran.strip() + vcl = [self.convert, '-pointsize 25','-fill maroon', + '-draw "%s"' % s, tmppng, outpng] + p=subprocess.Popen(' '.join(vcl),shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + s = '## executing %s returned %d\n' % (' '.join(vcl),retval) + self.lf.write(s) + try: + os.remove(os.path.join(self.outfpath,tmppng)) + except: + pass + nimages = len(glob.glob(os.path.join(self.outfpath,'*.png'))) # rely on HaploView shouting - PNG @! + self.lf.write('### nimages=%d\n' % nimages) + if nimages > 0: # haploview may fail? + vcl = '%s -format pdf -resize 800x400! *.png' % self.mogrify + p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + vcl = '%s *.pdf --fitpaper true --outfile alljoin.pdf' % self.pdfjoin + p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + vcl = '%s alljoin.pdf --nup 1x%d --outfile allnup.pdf' % (self.pdfnup,nimages) + p=subprocess.Popen(vcl,shell=True,cwd=self.outfpath,stderr=self.lf,stdout=self.lf) + retval = p.wait() + self.lf.write('## executing %s returned %d\n' % (vcl,retval)) + #vcl = ['convert', 'allnup.pdf', 'allnup.png'] # this fails - bad pdf? + #p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath) + #retval = p.wait() + #lf.write('## executing %s returned %d\n' % (vcl,retval)) + ste.close() # temp file used to catch haploview blather + hblather = open(blog,'r').readlines() # to catch the blather + os.unlink(blog) + if len(hblather) > 0: + self.lf.write('## In addition, Haploview complained:') + self.lf.write(''.join(hblather)) + self.lf.write('\n') + self.lf.close() + flist = glob.glob(os.path.join(self.outfpath, '*')) + flist.sort() + ts = '!"#$%&\'()*+,-/:;<=>?@[\\]^_`{|}~' + string.whitespace + ftran = string.maketrans(ts,'_'*len(ts)) + outf = file(self.outfile,'w') + outf.write(galhtmlprefix % progname) + s = '<h4>rgenetics for Galaxy %s, wrapping HaploView</h4>' % (progname) + outf.write(s) + """ + as at ashg 2009, convert fails on allnup.pdf - probably too complex... + mainthumb = 'allnup.png' + mainpdf = 'allnup.pdf' + if os.path.exists(mainpdf): + if not os.path.exists(mainthumb): + outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf)) + else: + outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">') + outf.write('</td><td>Click this thumbnail to display the main combined LD image</td></tr></table>\n' % (mainpdf,mainthumb)) + else: + outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n') + outf.write('## Called as %s' % sys.argv) + """ + outf.write('<br><div><hr><ul>\n') + for i, data in enumerate( flist ): + dn = os.path.split(data)[-1] + if dn[:3] <> 'all': + continue + newdn = dn.translate(ftran) + if dn <> newdn: + os.rename(os.path.join(self.outfpath,dn),os.path.join(self.outfpath,newdn)) + dn = newdn + dnlabel = dn + ext = dn.split('.')[-1] + if dn == 'allnup.pdf': + dnlabel = 'All pdf plots on a single page' + elif dn == 'alljoin.pdf': + dnlabel = 'All pdf plots, each on a separate page' + outf.write('<li><a href="%s">%s - %s</a></li>\n' % (dn,dn,dnlabel)) + for i, data in enumerate( flist ): + dn = os.path.split(data)[-1] + if dn[:3] == 'all': + continue + newdn = dn.translate(ftran) + if dn <> newdn: + os.rename(os.path.join(self.outfpath,dn),os.path.join(self.outfpath,newdn)) + dn = newdn + dnlabel = dn + ext = dn.split('.')[-1] + if dn == 'allnup.pdf': + dnlabel = 'All pdf plots on a single page' + elif dn == 'alljoin.pdf': + dnlabel = 'All pdf plots, each on a separate page' + elif ext == 'info': + dnlabel = '%s map data for Haploview input' % self.title + elif ext == 'ped': + dnlabel = '%s genotype data for Haploview input' % self.title + elif dn.find('CEU') <> -1 or dn.find('YRI') <> -1 or dn.find('CHB_JPT') <> -1: # is hapmap + dnlabel = 'Hapmap data' + if ext == 'TAGS' or ext == 'TESTS' or ext == 'CHAPS': + dnlabel = dnlabel + ' Tagger output' + outf.write('<li><a href="%s">%s - %s</a></li>\n' % (dn,dn,dnlabel)) + outf.write('</ol><br>') + outf.write("</div><div><hr>Job Log follows below (see %s)<pre>" % self.logfn) + s = file(self.log_file,'r').readlines() + s = '\n'.join(s) + outf.write('%s</pre><hr></div>' % s) + outf.write('</body></html>') + outf.close() + if self.useTemp: + try: + os.unlink(self.tempMapName) + os.unlink(self.tempPedName) + except: + pass + +if __name__ == "__main__": """ ### Sanity check the arguments <command interpreter="python"> @@ -52,444 +507,11 @@ def ld(): skipcheck? """ progname = os.path.split(sys.argv[0])[-1] - ts = '%s%s' % (string.punctuation,string.whitespace) - ptran = string.maketrans(ts,'_'*len(ts)) if len(sys.argv) < 16: s = '##!%s: Expected 16 params in sys.argv, got %d (%s)' % (progname,len(sys.argv), sys.argv) print s sys.exit(1) + ld = ldPlot(argv = sys.argv) + ld.doPlots() - ### Figure out what genomic region we are interested in - region = sys.argv[1] - orslist = sys.argv[2].replace('X',' ').lower() # galaxy replaces newlines with XX - go figure - title = sys.argv[3].translate(ptran) - # for outputs - outfile = sys.argv[4] - logfn = 'Log_%s.txt' % (title) - histextra = sys.argv[5] - base_name = sys.argv[6] - pedFileBase = os.path.join(histextra,base_name) - print 'pedfilebase=%s' % pedFileBase - minMaf=sys.argv[7] - if minMaf: - try: - minMaf = float(minMaf) - except: - minMaf = 0.0 - maxDist=sys.argv[8] or None - ldType=sys.argv[9] or 'RSQ' - hiRes = (sys.argv[10].lower() == 'hi') - memSize= sys.argv[11] or '1000' - memSize = int(memSize) - outfpath = sys.argv[12] - infotrack = False # note that otherwise this breaks haploview in headless mode - #infotrack = sys.argv[13] == 'info' - # this fails in headless mode as at april 2010 with haploview 4.2 - tagr2 = sys.argv[14] or '0.8' - hmpanels = sys.argv[15] # eg "['CEU','YRI']" - if hmpanels: - hmpanels = hmpanels.replace('[','') - hmpanels = hmpanels.replace(']','') - hmpanels = hmpanels.replace("'",'') - hmpanels = hmpanels.split(',') - hvbin = sys.argv[16] # added rml june 2008 - bindir = os.path.split(hvbin)[0] - # jan 2010 - always assume utes are on path to avoid platform problems - pdfjoin = 'pdfjoin' # os.path.join(bindir,'pdfjoin') - pdfnup = 'pdfnup' # os.path.join(bindir,'pdfnup') - mogrify = 'mogrify' # os.path.join(bindir,'mogrify') - convert = 'convert' # os.path.join(bindir,'convert') - log_file = os.path.join(outfpath,logfn) - MAP_FILE = '%s.map' % pedFileBase - DATA_FILE = '%s.ped' % pedFileBase - try: - os.makedirs(outfpath) - s = '## made new path %s\n' % outfpath - except: - pass - lf = file(log_file,'w') - s = 'PATH=%s\n' % os.environ.get('PATH','?') - lf.write(s) - hlogf = os.path.join(outfpath,'%s.log' % pedFileBase) - chromosome = '' - spos = epos = -9 - rslist = [] - rsdict = {} - hlog = [] - if region > '': - useRs = [] - useRsdict={} - try: # TODO make a regexp? - c,rest = region.split(':') - chromosome = c.replace('chr','') - rest = rest.replace(',','') # remove commas - spos,epos = rest.split('-') - spos = int(spos) - epos = int(epos) - s = '## %s parsing chrom %s from %d to %d\n' % (progname,chromosome,spos,epos) - lf.write(s) - lf.write('\n') - print >> sys.stdout, s - except: - s = '##! %s unable to parse region %s - MUST look like "chr8:10,000-100,000\n' % (progname,region) - print >> sys.stdout, s - lf.write(s) - lf.write('\n') - lf.close() - sys.exit(1) - else: - useRs = orslist.split() # galaxy replaces newlines with XX - go figure - useRsdict = dict(zip(useRs,useRs)) - useTemp = False - try: - dfile = open(DATA_FILE, 'r') - except: # bad input file name? - s = '##! RGeno unable to open file %s\n' % (DATA_FILE) - lf.write(s) - lf.write('\n') - lf.close() - print >> sys.stdout, s - raise - sys.exit(1) - try: - mfile = open(MAP_FILE, 'r') - except: # bad input file name? - s = '##! RGeno unable to open file %s' % (MAP_FILE) - lf.write(s) - lf.write('\n') - lf.close() - print >> sys.stdout, s - raise - sys.exit(1) - if len(useRs) > 0 or spos <> -9 : # subset region - useTemp = True - ### Figure out which markers are in this region - markers = [] - snpcols = {} - chroms = {} - minpos = 2**32 - maxpos = 0 - for lnum,row in enumerate(mfile): - line = row.strip() - if not line: continue - chrom, snp, genpos, abspos = line.split() - try: - ic = int(chrom) - except: - ic = None - if ic and ic <= 23: - try: - abspos = int(abspos) - if abspos > maxpos: - maxpos = abspos - if abspos < minpos: - minpos = abspos - except: - abspos = epos + 999999999 # so next test fails - if useRsdict.get(snp,None) or (spos <> -9 and chrom == chromosome and (spos <= abspos <= epos)): - if chromosome == '': - chromosome = chrom - chroms.setdefault(chrom,chrom) - markers.append((chrom,abspos,snp)) # decorate for sort into genomic - snpcols[snp] = lnum # so we know which col to find genos for this marker - markers.sort() - rslist = [x[2] for x in markers] # drop decoration - rsdict = dict(zip(rslist,rslist)) - if len(rslist) == 0: - s = '##! %s found no rs numbers in %s' % (progname,sys.argv[1:3]) - lf.write(s) - lf.write('\n') - lf.close() - print >> sys.stdout, s - sys.exit(1) - if spos == -9: - spos = minpos - epos = maxpos - s = '## %s looking for %d rs (%s)' % (progname,len(rslist),rslist[:5]) - lf.write(s) - print >> sys.stdout, s - wewant = [(6+(2*snpcols[x])) for x in rslist] # - # column indices of first geno of each marker pair to get the markers into genomic - ### ... and then parse the rest of the ped file to pull out - ### the genotypes for all subjects for those markers - # /usr/local/galaxy/data/rg/1/lped/ - tempMapName = os.path.join(outfpath,'%s.info' % title) - tempMap = file(tempMapName,'w') - tempPedName = os.path.join(outfpath,'%s.ped' % title) - tempPed = file(tempPedName,'w') - pngpath = '%s.LD.PNG' % tempPedName - map = ['%s\t%s' % (x[2],x[1]) for x in markers] # snp,abspos in genomic order for haploview - tempMap.write('%s\n' % '\n'.join(map)) - tempMap.close() - nrows = 0 - for line in dfile: - line = line.strip() - if not line: - continue - fields = line.split() - preamble = fields[:6] - g = ['%s %s' % (fields[snpcol], fields[snpcol+1]) for snpcol in wewant] - g = ' '.join(g) - g = g.split() # we'll get there - g = [atrandic.get(x,'0') for x in g] # numeric alleles... - tempPed.write('%s %s\n' % (' '.join(preamble), ' '.join(g))) - nrows += 1 - tempPed.close() - s = '## %s: wrote %d markers, %d subjects for region %s\n' % (progname,len(rslist),nrows,region) - lf.write(s) - lf.write('\n') - print >> sys.stdout,s - else: # even if using all, must set up haploview info file instead of map - markers = [] - chroms = {} - spos = sys.maxint - epos = -spos - for lnum,row in enumerate(mfile): - line = row.strip() - if not line: continue - chrom, snp, genpos, abspos = line.split() - try: - ic = int(chrom) - except: - ic = None - if ic and ic <= 23: - if chromosome == '': - chromosome = chrom - chroms.setdefault(chrom,chrom) - try: - p = int(abspos) - if p < spos and p <> 0: - spos = p - if p > epos and p <> 0: - epos = p - except: - pass - markers.append('%s %s' % (snp,abspos)) # no sort - pass - # now have spos and epos for hapmap if hmpanels - tempMapName = os.path.join(outfpath,'%s.info' % title) - tempMap = file(tempMapName,'w') - tempMap.write('\n'.join(markers)) - tempMap.close() - tempPedName = os.path.join(outfpath,'%s.ped' % title) - try: # will fail on winblows! - os.symlink(DATA_FILE,tempPedName) - except: - shutil.copy(DATA_FILE,tempPedName) # wasteful but.. - nchroms = len(chroms) # if > 1 can't really do this safely - if nchroms > 1: - s = '## warning - multiple chromosomes found in your map file - %s\n' % ','.join(chroms.keys()) - lf.write(s) - print >> sys.stdout,s - sys.exit(1) - DATA_FILE = tempPedName # for haploview - INFO_FILE = tempMapName - dfile.close() - mfile.close() - fblog,blog = tempfile.mkstemp() - ste = open(blog,'w') # to catch the blather - # if no need to rewrite - set up names for haploview call - vcl = [javabin,'-jar',hvbin,'-n','-memory','%d' % memSize,'-pairwiseTagging', - '-pedfile',DATA_FILE,'-info',INFO_FILE,'-tagrsqcounts', - '-tagrsqcutoff',tagr2, - '-ldcolorscheme',ldType] - if minMaf: - vcl += ['-minMaf','%f' % minMaf] - if maxDist: - vcl += ['-maxDistance',maxDist] - if hiRes: - vcl.append('-png') - else: - vcl.append('-compressedpng') - if nchroms == 1: - vcl += ['-chromosome',chromosome] - if infotrack: - vcl.append('-infoTrack') - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=ste,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - vcl = [mogrify, '-resize 800x400!', '*.PNG'] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - inpng = '%s.LD.PNG' % DATA_FILE # stupid but necessary - can't control haploview name mangle - inpng = inpng.replace(' ','') - inpng = os.path.split(inpng)[-1] - tmppng = '%s.tmp.png' % title - tmppng = tmppng.replace(' ','') - outpng = '1_%s.png' % title - outpng = outpng.replace(' ','') - outpng = os.path.split(outpng)[-1] - vcl = [convert, '-resize 800x400!', inpng, tmppng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - s = "text 10,300 '%s'" % title[:40] - vcl = ['convert', '-pointsize 25','-fill maroon', - '-draw "%s"' % s, tmppng, outpng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - try: - os.remove(os.path.join(outfpath,tmppng)) - except: - pass # label all the plots then delete all the .PNG files before munging - fnum=1 - if hmpanels: - sp = '%d' % (spos/1000.) # hapmap wants kb - ep = '%d' % (epos/1000.) - for panel in hmpanels: - if panel > '' and panel.lower() <> 'none': # in case someone checks that option too :) - ptran = panel.strip() - ptran = ptran.replace('+','_') - fnum += 1 # preserve an order or else we get sorted - vcl = [javabin,'-jar',hvbin,'-n','-memory','%d' % memSize, - '-chromosome',chromosome, '-panel',panel.strip(), - '-hapmapDownload','-startpos',sp,'-endpos',ep, - '-ldcolorscheme',ldType] - if minMaf: - vcl += ['-minMaf','%f' % minMaf] - if maxDist: - vcl += ['-maxDistance',maxDist] - if hiRes: - vcl.append('-png') - else: - vcl.append('-compressedpng') - if infotrack: - vcl.append('-infoTrack') - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=ste,stdout=lf) - retval = p.wait() - inpng = 'Chromosome%s%s.LD.PNG' % (chromosome,panel) - inpng = inpng.replace(' ','') # mysterious spaces! - outpng = '%d_HapMap_%s_%s.png' % (fnum,ptran,chromosome,) - # hack for stupid chb+jpt - outpng = outpng.replace(' ','') - tmppng = '%s.tmp.png' % title - tmppng = tmppng.replace(' ','') - outpng = os.path.split(outpng)[-1] - vcl = [convert, '-resize 800x400!', inpng, tmppng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - s = "text 10,300 'HapMap %s'" % ptran.strip() - vcl = [convert, '-pointsize 25','-fill maroon', - '-draw "%s"' % s, tmppng, outpng] - p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - s = '## executing %s returned %d\n' % (' '.join(vcl),retval) - lf.write(s) - try: - os.remove(os.path.join(outfpath,tmppng)) - except: - pass - nimages = len(glob.glob(os.path.join(outfpath,'*.png'))) # rely on HaploView shouting - PNG @! - lf.write('### nimages=%d\n' % nimages) - if nimages > 0: # haploview may fail? - vcl = '%s -format pdf -resize 800x400! *.png' % mogrify - p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - lf.write('## executing %s returned %d\n' % (vcl,retval)) - vcl = '%s *.pdf --fitpaper true --outfile alljoin.pdf' % pdfjoin - p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - lf.write('## executing %s returned %d\n' % (vcl,retval)) - vcl = '%s alljoin.pdf --nup 1x%d --outfile allnup.pdf' % (pdfnup,nimages) - p=subprocess.Popen(vcl,shell=True,cwd=outfpath,stderr=lf,stdout=lf) - retval = p.wait() - lf.write('## executing %s returned %d\n' % (vcl,retval)) - #vcl = ['convert', 'allnup.pdf', 'allnup.png'] # this fails - bad pdf? - #p=subprocess.Popen(' '.join(vcl),shell=True,cwd=outfpath) - #retval = p.wait() - #lf.write('## executing %s returned %d\n' % (vcl,retval)) - lf.write('\n'.join(hlog)) - ste.close() # temp file used to catch haploview blather - hblather = open(blog,'r').readlines() # to catch the blather - os.unlink(blog) - if len(hblather) > 0: - lf.write('## In addition, Haploview complained:') - lf.write(''.join(hblather)) - lf.write('\n') - lf.close() - flist = glob.glob(os.path.join(outfpath, '*')) - flist.sort() - ts = '!"#$%&\'()*+,-/:;<=>?@[\\]^_`{|}~' + string.whitespace - ftran = string.maketrans(ts,'_'*len(ts)) - outf = file(outfile,'w') - outf.write(galhtmlprefix % progname) - s = '<h4>rgenetics for Galaxy %s, wrapping HaploView</h4>' % (progname) - outf.write(s) - """ - as at ashg 2009, convert fails on allnup.pdf - probably too complex... - mainthumb = 'allnup.png' - mainpdf = 'allnup.pdf' - if os.path.exists(mainpdf): - if not os.path.exists(mainthumb): - outf.write('<table><tr><td colspan="3"><a href="%s">Main combined LD plot</a></td></tr></table>\n' % (mainpdf)) - else: - outf.write('<table><tr><td><a href="%s"><img src="%s" alt="Main combined LD image" hspace="10" align="middle">') - outf.write('</td><td>Click this thumbnail to display the main combined LD image</td></tr></table>\n' % (mainpdf,mainthumb)) - else: - outf.write('(No main image was generated - this usually means a Haploview error connecting to Hapmap site - please try later)<br/>\n') - outf.write('## Called as %s' % sys.argv) - """ - outf.write('<br><div><hr><ul>\n') - for i, data in enumerate( flist ): - dn = os.path.split(data)[-1] - if dn[:3] <> 'all': - continue - newdn = dn.translate(ftran) - if dn <> newdn: - os.rename(os.path.join(outfpath,dn),os.path.join(outfpath,newdn)) - dn = newdn - dnlabel = dn - ext = dn.split('.')[-1] - if dn == 'allnup.pdf': - dnlabel = 'All pdf plots on a single page' - elif dn == 'alljoin.pdf': - dnlabel = 'All pdf plots, each on a separate page' - outf.write('<li><a href="%s">%s - %s</a></li>\n' % (dn,dn,dnlabel)) - for i, data in enumerate( flist ): - dn = os.path.split(data)[-1] - if dn[:3] == 'all': - continue - newdn = dn.translate(ftran) - if dn <> newdn: - os.rename(os.path.join(outfpath,dn),os.path.join(outfpath,newdn)) - dn = newdn - dnlabel = dn - ext = dn.split('.')[-1] - if dn == 'allnup.pdf': - dnlabel = 'All pdf plots on a single page' - elif dn == 'alljoin.pdf': - dnlabel = 'All pdf plots, each on a separate page' - elif ext == 'info': - dnlabel = '%s map data for Haploview input' % title - elif ext == 'ped': - dnlabel = '%s genotype data for Haploview input' % title - elif dn.find('CEU') <> -1 or dn.find('YRI') <> -1 or dn.find('CHB_JPT') <> -1: # is hapmap - dnlabel = 'Hapmap data' - if ext == 'TAGS' or ext == 'TESTS' or ext == 'CHAPS': - dnlabel = dnlabel + ' Tagger output' - outf.write('<li><a href="%s">%s - %s</a></li>\n' % (dn,dn,dnlabel)) - outf.write('</ol><br>') - outf.write("</div><div><hr>Job Log follows below (see %s)<pre>" % logfn) - s = file(log_file,'r').readlines() - s = '\n'.join(s) - outf.write('%s</pre><hr></div>' % s) - outf.write('</body></html>') - outf.close() - if useTemp: - try: - os.unlink(tempMapName) - os.unlink(tempPedName) - except: - pass - -if __name__ == "__main__": - ld() -

1 0

galaxy-dist commit 2f02897723c2: Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289246454 18000 # Node ID 2f02897723c2f3c1d0d7be8c14f4c664409e1c59 # Parent 1ebd342fb4eb29c095b19a960503402f75cbe944 Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers --- a/tools/samtools/sam_merge.xml +++ b/tools/samtools/sam_merge.xml @@ -4,7 +4,7 @@ <requirement type="package">samtools</requirement></requirements><command interpreter="python"> - sam_merge.py + sam_merge.py $input1 $output1 $input2 @@ -40,7 +40,7 @@ <test><param name="input1" value="sam_merge_in1.bam" ftype="bam" /><param name="input2" value="sam_merge_in2.bam" ftype="bam" /> --- a/tools/samtools/sam_to_bam.xml +++ b/tools/samtools/sam_to_bam.xml @@ -4,13 +4,16 @@ <requirement type="package">samtools</requirement></requirements><command interpreter="python"> -sam_to_bam.py --input1=$source.input1 --dbkey=${input1.metadata.dbkey} -#if $source.index_source == "history": ---ref_file=$source.ref_file -#else ---ref_file="None" -#end if ---output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} + sam_to_bam.py + --input1=$source.input1 + --dbkey=${input1.metadata.dbkey} + #if $source.index_source == "history": + --ref_file=$source.ref_file + #else + --ref_file="None" + #end if + --output1=$output1 + --index_dir=${GALAXY_DATA_INDEX_DIR} </command><inputs><conditional name="source"> --- a/test-data/sam_pileup_out2.pileup +++ b/test-data/sam_pileup_out2.pileup @@ -1,224 +1,224 @@ -chrM 23 A A 25 0 25 1 ^:. I -chrM 24 A A 25 0 25 1 . I -chrM 25 G G 25 0 25 1 . I -chrM 26 C C 25 0 25 1 . I -chrM 27 A A 25 0 25 1 . I -chrM 28 A A 25 0 25 1 . I -chrM 29 G G 25 0 25 1 . I -chrM 30 G A 4 4 25 1 N " -chrM 31 C A 4 4 25 1 N " -chrM 32 A A 25 0 25 1 . I -chrM 33 C C 25 0 25 1 . I -chrM 34 T T 25 0 25 1 . I -chrM 35 G G 25 0 25 1 . I -chrM 36 A A 25 0 25 1 . I -chrM 37 A A 25 0 25 1 . I -chrM 38 A A 25 0 25 1 . I -chrM 39 A A 25 0 25 1 . I -chrM 40 T T 25 0 25 1 . I -chrM 41 G G 25 0 25 1 . I -chrM 42 C C 25 0 25 1 . I -chrM 43 C C 25 0 25 1 . I -chrM 44 T T 25 0 25 1 . I -chrM 45 A A 25 0 25 1 . I -chrM 46 G G 25 0 25 1 . I -chrM 47 A A 25 0 25 1 . E -chrM 48 T T 25 0 25 1 . I -chrM 49 G G 25 0 25 1 . I -chrM 50 A A 25 0 25 1 . I -chrM 51 G G 25 0 25 1 . I -chrM 52 T T 25 0 25 1 . I -chrM 53 A A 25 0 25 1 . I -chrM 54 T T 25 0 25 1 . I -chrM 55 T T 25 0 25 1 . I -chrM 56 C C 25 0 25 1 . I -chrM 57 T T 25 0 25 1 . I -chrM 58 T T 25 0 25 1 .$ I -chrM 96 T T 25 0 25 1 ^:. I -chrM 97 T T 25 0 25 1 . I -chrM 98 A A 25 0 25 1 . I -chrM 99 G G 25 0 25 1 . I -chrM 100 T T 25 0 25 1 . I -chrM 101 T T 25 0 25 1 . I -chrM 102 A A 25 0 25 1 . I -chrM 103 T A 4 4 25 1 N " -chrM 104 T A 4 4 25 1 N " -chrM 105 A A 25 0 25 1 . I -chrM 106 A A 25 0 25 1 . I -chrM 107 T T 25 0 25 1 . I -chrM 108 A A 25 0 25 1 . I -chrM 109 G G 25 0 25 1 . I -chrM 110 A A 25 0 25 1 . I -chrM 111 A A 25 0 25 1 . I -chrM 112 T T 25 0 25 1 . I -chrM 113 T T 25 0 25 1 . I -chrM 114 A A 25 0 25 1 . I -chrM 115 C C 25 0 25 1 . I -chrM 116 A A 25 0 25 1 . I -chrM 117 C C 25 0 25 1 . I -chrM 118 A A 25 0 25 1 . H -chrM 119 T T 25 0 25 1 . I -chrM 120 G G 25 0 25 1 . I -chrM 121 C C 25 0 25 1 . I -chrM 122 A A 25 0 25 1 . E -chrM 123 A A 25 0 25 1 . I -chrM 124 G G 20 0 25 1 . 5 -chrM 125 T T 25 0 25 1 . I -chrM 126 A A 25 0 25 1 . I -chrM 127 T T 25 0 25 1 . I -chrM 128 C C 25 0 25 1 . I -chrM 129 C C 25 0 25 1 . I -chrM 130 G G 19 0 25 1 . 4 -chrM 131 C C 25 0 25 1 .$ I -chrM 492 A A 25 0 25 1 ^:, I -chrM 493 A A 25 0 25 1 , I -chrM 494 A A 25 0 25 1 , I -chrM 495 C C 25 0 25 1 , E -chrM 496 T T 25 0 25 1 , I -chrM 497 G G 25 0 25 1 , I -chrM 498 G G 25 0 25 1 , I -chrM 499 G G 25 0 25 1 , I -chrM 500 A A 25 0 25 1 , I -chrM 501 T T 25 0 25 1 , I -chrM 502 T T 25 0 25 1 , I -chrM 503 A A 25 0 25 1 , I -chrM 504 G G 25 0 25 1 , I -chrM 505 A A 25 0 25 1 , I -chrM 506 T T 25 0 25 1 , I -chrM 507 A A 25 0 25 1 , I -chrM 508 C C 25 0 25 1 , I -chrM 509 C C 25 0 25 1 , I -chrM 510 C C 25 0 25 1 , I -chrM 511 C C 25 0 25 1 , I -chrM 512 A A 25 0 25 1 , I -chrM 513 C C 25 0 25 1 , I -chrM 514 T T 25 0 25 1 , I -chrM 515 A A 25 0 25 1 , I -chrM 516 T T 25 0 25 1 , I -chrM 517 G G 25 0 25 1 , I -chrM 518 C C 25 0 25 1 , I -chrM 519 T A 4 4 25 1 n " -chrM 520 T A 4 4 25 1 n " -chrM 521 A A 25 0 25 1 , I -chrM 522 G G 25 0 25 1 , I -chrM 523 C C 25 0 25 1 , I -chrM 524 C C 25 0 25 1 , I -chrM 525 C C 25 0 25 1 , I -chrM 526 T T 25 0 25 1 , I -chrM 527 A A 25 0 25 1 ,$ I -chrM 893 G G 21 0 25 1 ^:, 6 -chrM 894 C C 15 0 25 1 , 0 -chrM 895 T T 19 0 25 1 , 4 -chrM 896 T T 25 0 25 1 , I -chrM 897 A A 25 0 25 1 , I -chrM 898 A A 25 0 25 1 , I -chrM 899 T T 25 0 25 1 , ? -chrM 900 T T 25 0 25 1 , I -chrM 901 G G 25 0 25 1 , I -chrM 902 A A 25 0 25 1 , I -chrM 903 A A 25 0 25 1 , I -chrM 904 T T 25 0 25 1 , < -chrM 905 C C 25 0 25 1 , I -chrM 906 A A 25 0 25 1 , I -chrM 907 G G 25 0 25 1 , I -chrM 908 G G 25 0 25 1 , I -chrM 909 C C 25 0 25 1 , I -chrM 910 C C 25 0 25 1 , I -chrM 911 A A 25 0 25 1 , I -chrM 912 T T 25 0 25 1 , I -chrM 913 G G 25 0 25 1 , I -chrM 914 A A 25 0 25 1 , I -chrM 915 A A 25 0 25 1 , I -chrM 916 G G 25 0 25 1 , I -chrM 917 C C 25 0 25 1 , I -chrM 918 G G 25 0 25 1 , I -chrM 919 C C 25 0 25 1 , I -chrM 920 G A 4 4 25 1 n " -chrM 921 C A 4 4 25 1 n " -chrM 922 A A 25 0 25 1 , I -chrM 923 C C 25 0 25 1 , I -chrM 924 A A 25 0 25 1 , I -chrM 925 C C 25 0 25 1 , I -chrM 926 A A 25 0 25 1 , I -chrM 927 C C 25 0 25 1 , I -chrM 928 C C 25 0 25 1 ,$ I -chrM 1159 T T 25 0 25 1 ^:. I -chrM 1160 T T 25 0 25 1 . I -chrM 1161 A A 25 0 25 1 . I -chrM 1162 A A 25 0 25 1 . I -chrM 1163 C C 25 0 25 1 . I -chrM 1164 T T 25 0 25 1 . I -chrM 1165 A A 25 0 25 1 . I -chrM 1166 A A 4 0 25 1 N " -chrM 1167 A A 4 0 25 1 N " -chrM 1168 A A 25 0 25 1 . I -chrM 1169 C C 25 0 25 1 . I -chrM 1170 A A 25 0 25 1 . I -chrM 1171 T T 25 0 25 1 . I -chrM 1172 T T 25 0 25 1 . I -chrM 1173 C C 25 0 25 1 . I -chrM 1174 A A 25 0 25 1 . I -chrM 1175 C C 25 0 25 1 . I -chrM 1176 C C 25 0 25 1 . I -chrM 1177 A A 25 0 25 1 . I -chrM 1178 A A 25 0 25 1 . I -chrM 1179 A A 25 0 25 1 . A -chrM 1180 C C 25 0 25 1 . I -chrM 1181 C C 25 0 25 1 . I -chrM 1182 A A 25 0 25 1 . = -chrM 1183 T T 25 0 25 1 . I -chrM 1184 T T 25 0 25 1 . I -chrM 1185 A A 25 0 25 1 . B -chrM 1186 A A 20 0 25 1 . 5 -chrM 1187 A A 23 0 25 1 . 8 -chrM 1188 G G 25 0 25 1 . I -chrM 1189 T T 25 0 25 1 . = -chrM 1190 A A 25 0 25 1 . < -chrM 1191 T T 25 0 25 1 . I -chrM 1192 A A 33 0 25 2 .^:. ;I -chrM 1193 G G 33 0 25 2 .. II -chrM 1194 G G 33 0 25 2 .$. II -chrM 1195 A A 25 0 25 1 . I -chrM 1196 G G 25 0 25 1 . I -chrM 1197 A A 25 0 25 1 . I -chrM 1198 T T 25 0 25 1 . I -chrM 1199 A A 4 0 25 1 N " -chrM 1200 G A 4 4 25 1 N " -chrM 1201 A A 25 0 25 1 . I -chrM 1202 A A 25 0 25 1 . I -chrM 1203 A A 25 0 25 1 . I -chrM 1204 T T 25 0 25 1 . I -chrM 1205 T T 25 0 25 1 . I -chrM 1206 T T 25 0 25 1 . I -chrM 1207 T T 25 0 25 1 . I -chrM 1208 A A 25 0 25 1 . I -chrM 1209 A A 25 0 25 1 . I -chrM 1210 C C 25 0 25 1 . I -chrM 1211 T T 25 0 25 1 . I -chrM 1212 T T 25 0 25 1 . I -chrM 1213 G G 25 0 25 1 . I -chrM 1214 G G 25 0 25 1 . I -chrM 1215 C C 25 0 25 1 . I -chrM 1216 G G 25 0 25 1 . I -chrM 1217 C C 25 0 25 1 . I -chrM 1218 T T 25 0 25 1 . I -chrM 1219 A A 25 0 25 1 . I -chrM 1220 T T 25 0 25 1 . I -chrM 1221 A A 25 0 25 1 . C -chrM 1222 G G 25 0 25 1 . < -chrM 1223 A A 25 0 25 1 . I -chrM 1224 G G 25 0 25 1 . H -chrM 1225 A A 25 0 25 1 . I -chrM 1226 A A 25 0 25 1 . I -chrM 1227 A A 25 0 25 1 .$ I -chrM 1499 A A 25 0 25 1 ^:, I -chrM 1500 A A 25 0 25 1 , I -chrM 1501 A A 25 0 25 1 , I -chrM 1502 T T 25 0 25 1 , I -chrM 1503 T T 33 0 25 2 ,^:, EI -chrM 1504 T T 33 0 25 2 ,, II +chrM 23 A A 30 0 25 1 ^:. > +chrM 24 A A 30 0 25 1 . > +chrM 25 G G 30 0 25 1 . I +chrM 26 C C 30 0 25 1 . I +chrM 27 A A 30 0 25 1 . I +chrM 28 A A 30 0 25 1 . I +chrM 29 G G 30 0 25 1 . I +chrM 30 G N 0 0 0 1 N " +chrM 31 C N 0 0 0 1 N " +chrM 32 A A 30 0 25 1 . I +chrM 33 C C 30 0 25 1 . I +chrM 34 T T 30 0 25 1 . I +chrM 35 G G 30 0 25 1 . I +chrM 36 A A 30 0 25 1 . I +chrM 37 A A 30 0 25 1 . I +chrM 38 A A 30 0 25 1 . I +chrM 39 A A 30 0 25 1 . I +chrM 40 T T 30 0 25 1 . I +chrM 41 G G 30 0 25 1 . I +chrM 42 C C 30 0 25 1 . I +chrM 43 C C 30 0 25 1 . I +chrM 44 T T 30 0 25 1 . I +chrM 45 A A 30 0 25 1 . I +chrM 46 G G 30 0 25 1 . I +chrM 47 A A 30 0 25 1 . E +chrM 48 T T 30 0 25 1 . I +chrM 49 G G 30 0 25 1 . I +chrM 50 A A 30 0 25 1 . I +chrM 51 G G 30 0 25 1 . I +chrM 52 T T 30 0 25 1 . I +chrM 53 A A 30 0 25 1 . I +chrM 54 T T 30 0 25 1 . I +chrM 55 T T 30 0 25 1 . I +chrM 56 C C 30 0 25 1 . I +chrM 57 T T 30 0 25 1 . E +chrM 58 T T 30 0 25 1 .$ B +chrM 96 T T 30 0 25 1 ^:. B +chrM 97 T T 30 0 25 1 . E +chrM 98 A A 30 0 25 1 . I +chrM 99 G G 30 0 25 1 . I +chrM 100 T T 30 0 25 1 . I +chrM 101 T T 30 0 25 1 . I +chrM 102 A A 30 0 25 1 . I +chrM 103 T N 0 0 0 1 N " +chrM 104 T N 0 0 0 1 N " +chrM 105 A A 30 0 25 1 . I +chrM 106 A A 30 0 25 1 . I +chrM 107 T T 30 0 25 1 . I +chrM 108 A A 30 0 25 1 . I +chrM 109 G G 30 0 25 1 . I +chrM 110 A A 30 0 25 1 . I +chrM 111 A A 30 0 25 1 . I +chrM 112 T T 30 0 25 1 . I +chrM 113 T T 30 0 25 1 . I +chrM 114 A A 30 0 25 1 . I +chrM 115 C C 30 0 25 1 . I +chrM 116 A A 30 0 25 1 . I +chrM 117 C C 30 0 25 1 . I +chrM 118 A A 30 0 25 1 . H +chrM 119 T T 30 0 25 1 . I +chrM 120 G G 30 0 25 1 . I +chrM 121 C C 30 0 25 1 . I +chrM 122 A A 30 0 25 1 . E +chrM 123 A A 30 0 25 1 . I +chrM 124 G G 30 0 25 1 . 5 +chrM 125 T T 30 0 25 1 . I +chrM 126 A A 30 0 25 1 . I +chrM 127 T T 30 0 25 1 . I +chrM 128 C C 30 0 25 1 . I +chrM 129 C C 30 0 25 1 . I +chrM 130 G G 30 0 25 1 . 4 +chrM 131 C C 30 0 25 1 .$ C +chrM 492 A A 30 0 25 1 ^:, A +chrM 493 A A 30 0 25 1 , B +chrM 494 A A 30 0 25 1 , E +chrM 495 C C 30 0 25 1 , E +chrM 496 T T 30 0 25 1 , I +chrM 497 G G 30 0 25 1 , I +chrM 498 G G 30 0 25 1 , I +chrM 499 G G 30 0 25 1 , I +chrM 500 A A 30 0 25 1 , I +chrM 501 T T 30 0 25 1 , I +chrM 502 T T 30 0 25 1 , I +chrM 503 A A 30 0 25 1 , I +chrM 504 G G 30 0 25 1 , I +chrM 505 A A 30 0 25 1 , I +chrM 506 T T 30 0 25 1 , I +chrM 507 A A 30 0 25 1 , I +chrM 508 C C 30 0 25 1 , I +chrM 509 C C 30 0 25 1 , I +chrM 510 C C 30 0 25 1 , I +chrM 511 C C 30 0 25 1 , I +chrM 512 A A 30 0 25 1 , I +chrM 513 C C 30 0 25 1 , I +chrM 514 T T 30 0 25 1 , I +chrM 515 A A 30 0 25 1 , I +chrM 516 T T 30 0 25 1 , I +chrM 517 G G 30 0 25 1 , I +chrM 518 C C 30 0 25 1 , I +chrM 519 T N 0 0 0 1 n " +chrM 520 T N 0 0 0 1 n " +chrM 521 A A 30 0 25 1 , I +chrM 522 G G 30 0 25 1 , I +chrM 523 C C 30 0 25 1 , I +chrM 524 C C 30 0 25 1 , I +chrM 525 C C 30 0 25 1 , I +chrM 526 T T 30 0 25 1 , I +chrM 527 A A 30 0 25 1 ,$ > +chrM 893 G G 30 0 25 1 ^:, 6 +chrM 894 C C 30 0 25 1 , 0 +chrM 895 T T 30 0 25 1 , 4 +chrM 896 T T 30 0 25 1 , I +chrM 897 A A 30 0 25 1 , I +chrM 898 A A 30 0 25 1 , I +chrM 899 T T 30 0 25 1 , ? +chrM 900 T T 30 0 25 1 , I +chrM 901 G G 30 0 25 1 , I +chrM 902 A A 30 0 25 1 , I +chrM 903 A A 30 0 25 1 , I +chrM 904 T T 30 0 25 1 , < +chrM 905 C C 30 0 25 1 , I +chrM 906 A A 30 0 25 1 , I +chrM 907 G G 30 0 25 1 , I +chrM 908 G G 30 0 25 1 , I +chrM 909 C C 30 0 25 1 , I +chrM 910 C C 30 0 25 1 , I +chrM 911 A A 30 0 25 1 , I +chrM 912 T T 30 0 25 1 , I +chrM 913 G G 30 0 25 1 , I +chrM 914 A A 30 0 25 1 , I +chrM 915 A A 30 0 25 1 , I +chrM 916 G G 30 0 25 1 , I +chrM 917 C C 30 0 25 1 , I +chrM 918 G G 30 0 25 1 , I +chrM 919 C C 30 0 25 1 , I +chrM 920 G N 0 0 0 1 n " +chrM 921 C N 0 0 0 1 n " +chrM 922 A A 30 0 25 1 , I +chrM 923 C C 30 0 25 1 , I +chrM 924 A A 30 0 25 1 , I +chrM 925 C C 30 0 25 1 , I +chrM 926 A A 30 0 25 1 , I +chrM 927 C C 30 0 25 1 , E +chrM 928 C C 30 0 25 1 ,$ A +chrM 1159 T T 30 0 25 1 ^:. B +chrM 1160 T T 30 0 25 1 . E +chrM 1161 A A 30 0 25 1 . I +chrM 1162 A A 30 0 25 1 . I +chrM 1163 C C 30 0 25 1 . I +chrM 1164 T T 30 0 25 1 . I +chrM 1165 A A 30 0 25 1 . I +chrM 1166 A N 0 0 0 1 N " +chrM 1167 A N 0 0 0 1 N " +chrM 1168 A A 30 0 25 1 . I +chrM 1169 C C 30 0 25 1 . I +chrM 1170 A A 30 0 25 1 . I +chrM 1171 T T 30 0 25 1 . I +chrM 1172 T T 30 0 25 1 . I +chrM 1173 C C 30 0 25 1 . I +chrM 1174 A A 30 0 25 1 . I +chrM 1175 C C 30 0 25 1 . I +chrM 1176 C C 30 0 25 1 . I +chrM 1177 A A 30 0 25 1 . I +chrM 1178 A A 30 0 25 1 . I +chrM 1179 A A 30 0 25 1 . A +chrM 1180 C C 30 0 25 1 . I +chrM 1181 C C 30 0 25 1 . I +chrM 1182 A A 30 0 25 1 . = +chrM 1183 T T 30 0 25 1 . I +chrM 1184 T T 30 0 25 1 . I +chrM 1185 A A 30 0 25 1 . B +chrM 1186 A A 30 0 25 1 . 5 +chrM 1187 A A 30 0 25 1 . 8 +chrM 1188 G G 30 0 25 1 . I +chrM 1189 T T 30 0 25 1 . = +chrM 1190 A A 30 0 25 1 . < +chrM 1191 T T 30 0 25 1 . I +chrM 1192 A A 33 0 25 2 .^:. ;E +chrM 1193 G G 33 0 25 2 .. EI +chrM 1194 G G 33 0 25 2 .$. AI +chrM 1195 A A 30 0 25 1 . I +chrM 1196 G G 30 0 25 1 . I +chrM 1197 A A 30 0 25 1 . I +chrM 1198 T T 30 0 25 1 . I +chrM 1199 A N 0 0 0 1 N " +chrM 1200 G N 0 0 0 1 N " +chrM 1201 A A 30 0 25 1 . I +chrM 1202 A A 30 0 25 1 . I +chrM 1203 A A 30 0 25 1 . I +chrM 1204 T T 30 0 25 1 . I +chrM 1205 T T 30 0 25 1 . I +chrM 1206 T T 30 0 25 1 . I +chrM 1207 T T 30 0 25 1 . I +chrM 1208 A A 30 0 25 1 . I +chrM 1209 A A 30 0 25 1 . I +chrM 1210 C C 30 0 25 1 . I +chrM 1211 T T 30 0 25 1 . I +chrM 1212 T T 30 0 25 1 . I +chrM 1213 G G 30 0 25 1 . I +chrM 1214 G G 30 0 25 1 . I +chrM 1215 C C 30 0 25 1 . I +chrM 1216 G G 30 0 25 1 . I +chrM 1217 C C 30 0 25 1 . I +chrM 1218 T T 30 0 25 1 . I +chrM 1219 A A 30 0 25 1 . I +chrM 1220 T T 30 0 25 1 . I +chrM 1221 A A 30 0 25 1 . C +chrM 1222 G G 30 0 25 1 . < +chrM 1223 A A 30 0 25 1 . I +chrM 1224 G G 30 0 25 1 . H +chrM 1225 A A 30 0 25 1 . E +chrM 1226 A A 30 0 25 1 . B +chrM 1227 A A 30 0 25 1 .$ @ +chrM 1499 A A 30 0 25 1 ^:, A +chrM 1500 A A 30 0 25 1 , B +chrM 1501 A A 30 0 25 1 , E +chrM 1502 T T 30 0 25 1 , I +chrM 1503 T T 33 0 25 2 ,^:, E> +chrM 1504 T T 33 0 25 2 ,, I> chrM 1505 A A 33 0 25 2 ,, II -chrM 1506 C C 20 0 25 2 ,, +, +chrM 1506 C N 0 0 0 2 ,, +, chrM 1507 C C 33 0 25 2 ,, EH chrM 1508 T T 33 0 25 2 ,, II chrM 1509 A A 33 0 25 2 ,, II @@ -238,821 +238,821 @@ chrM 1522 T T 33 0 25 2 ,, II chrM 1523 T T 33 0 25 2 ,, II chrM 1524 C C 33 0 25 2 ,, II chrM 1525 T T 33 0 25 2 ,, II -chrM 1526 A A 28 0 25 2 n, "I -chrM 1527 A A 28 0 25 2 n, "I +chrM 1526 A A 30 0 25 2 n, "I +chrM 1527 A A 30 0 25 2 n, "I chrM 1528 T T 33 0 25 2 ,, II chrM 1529 G G 33 0 25 2 ,, II -chrM 1530 T T 19 0 25 2 ,n I" -chrM 1531 A A 28 0 25 2 ,n I" +chrM 1530 T T 30 0 25 2 ,n I" +chrM 1531 A A 30 0 25 2 ,n I" chrM 1532 A A 33 0 25 2 ,, II chrM 1533 A A 33 0 25 2 ,, II -chrM 1534 T T 33 0 25 2 ,$, II -chrM 1535 T T 25 0 25 1 , I -chrM 1536 T T 25 0 25 1 , I -chrM 1537 A A 25 0 25 1 , I -chrM 1538 A A 25 0 25 1 ,$ I -chrM 1616 A A 25 0 25 1 ^:. I -chrM 1617 G G 25 0 25 1 . I -chrM 1618 T T 25 0 25 1 . I -chrM 1619 T T 25 0 25 1 . I -chrM 1620 G G 25 0 25 1 . I -chrM 1621 G G 25 0 25 1 . I -chrM 1622 C C 25 0 25 1 . I -chrM 1623 T A 4 4 25 1 N " -chrM 1624 T A 4 4 25 1 N " -chrM 1625 A A 25 0 25 1 . I -chrM 1626 A A 25 0 25 1 . I -chrM 1627 A A 25 0 25 1 . I -chrM 1628 A A 25 0 25 1 . I -chrM 1629 G G 25 0 25 1 . I -chrM 1630 C C 25 0 25 1 . I -chrM 1631 A A 25 0 25 1 . I -chrM 1632 G G 25 0 25 1 . I -chrM 1633 C C 25 0 25 1 . I -chrM 1634 C C 25 0 25 1 . I -chrM 1635 A A 25 0 25 1 . C -chrM 1636 T T 25 0 25 1 . I -chrM 1637 C C 25 0 25 1 . I -chrM 1638 A A 25 0 25 1 . = -chrM 1639 A A 25 0 25 1 . G -chrM 1640 T T 25 0 25 1 . I -chrM 1641 T T 25 0 25 1 . I -chrM 1642 A A 25 0 25 1 . I -chrM 1643 A A 25 0 25 1 . I -chrM 1644 G G 25 0 25 1 . I -chrM 1645 A A 25 0 25 1 . @ -chrM 1646 A A 25 0 25 1 . I -chrM 1647 A A 25 0 25 1 . G -chrM 1648 G G 25 0 25 1 . I -chrM 1649 C C 25 0 25 1 . I -chrM 1650 G G 25 0 25 1 . I -chrM 1651 T T 25 0 25 1 .$ I -chrM 2261 C C 25 0 25 1 ^:, I -chrM 2262 A A 25 0 25 1 , I -chrM 2263 G G 25 0 25 1 , I -chrM 2264 C C 25 0 25 1 , I -chrM 2265 A A 25 0 25 1 , G -chrM 2266 A A 25 0 25 1 , I -chrM 2267 T T 17 0 25 1 , 2 -chrM 2268 T T 25 0 25 1 , = -chrM 2269 T T 18 0 25 1 , 3 -chrM 2270 C C 25 0 25 1 , I -chrM 2271 G G 25 0 25 1 , I -chrM 2272 G G 25 0 25 1 , I -chrM 2273 T T 25 0 25 1 , I -chrM 2274 T T 25 0 25 1 , I -chrM 2275 G G 25 0 25 1 , I -chrM 2276 G G 25 0 25 1 , I -chrM 2277 G G 25 0 25 1 , I -chrM 2278 G G 25 0 25 1 , I -chrM 2279 T T 25 0 25 1 , I -chrM 2280 G G 25 0 25 1 , I -chrM 2281 A A 25 0 25 1 , I -chrM 2282 C C 25 0 25 1 , I -chrM 2283 C C 25 0 25 1 , I -chrM 2284 T T 25 0 25 1 , I -chrM 2285 C C 25 0 25 1 , I -chrM 2286 G G 25 0 25 1 , I -chrM 2287 G G 25 0 25 1 , I -chrM 2288 A A 4 0 25 1 n " -chrM 2289 G A 4 4 25 1 n " -chrM 2290 A A 25 0 25 1 , I -chrM 2291 A A 25 0 25 1 , I -chrM 2292 C C 25 0 25 1 , I -chrM 2293 A A 25 0 25 1 , I -chrM 2294 A A 25 0 25 1 , I -chrM 2295 A A 25 0 25 1 , I -chrM 2296 A A 25 0 25 1 ,$ I -chrM 2334 A A 25 0 25 1 ^:, I -chrM 2335 A A 25 0 25 1 , I -chrM 2336 A A 25 0 25 1 , I -chrM 2337 T T 25 0 25 1 , I -chrM 2338 A A 25 0 25 1 , I -chrM 2339 T T 25 0 25 1 , H -chrM 2340 A A 25 0 25 1 , I -chrM 2341 T T 25 0 25 1 , = -chrM 2342 A A 25 0 25 1 , I -chrM 2343 A A 25 0 25 1 , I -chrM 2344 T T 25 0 25 1 , C -chrM 2345 C C 25 0 25 1 , I -chrM 2346 A A 25 0 25 1 , I -chrM 2347 C C 25 0 25 1 , I -chrM 2348 T T 25 0 25 1 , ? -chrM 2349 T T 25 0 25 1 , I -chrM 2350 A A 25 0 25 1 , I -chrM 2351 T T 25 0 25 1 , I -chrM 2352 T T 25 0 25 1 , I -chrM 2353 G G 25 0 25 1 , I -chrM 2354 A A 25 0 25 1 , I -chrM 2355 T T 25 0 25 1 , D -chrM 2356 C C 25 0 25 1 , I -chrM 2357 C C 25 0 25 1 , I -chrM 2358 A A 25 0 25 1 , I -chrM 2359 A A 25 0 25 1 , I -chrM 2360 A A 25 0 25 1 , I -chrM 2361 C A 4 4 25 1 n " -chrM 2362 C A 4 4 25 1 n " -chrM 2363 A A 25 0 25 1 , I -chrM 2364 T T 25 0 25 1 , I -chrM 2365 T T 25 0 25 1 , I -chrM 2366 G G 25 0 25 1 , I -chrM 2367 A A 25 0 25 1 , I -chrM 2368 T T 25 0 25 1 , I -chrM 2369 C C 25 0 25 1 ,$ I -chrM 2389 G G 25 0 25 1 ^:, I -chrM 2390 G G 23 0 25 1 , 8 -chrM 2391 G G 25 0 25 1 , I -chrM 2392 A A 25 0 25 1 , I -chrM 2393 T T 25 0 25 1 , I -chrM 2394 A A 25 0 25 1 , I -chrM 2395 A A 25 0 25 1 , I -chrM 2396 C C 23 0 25 1 , 8 -chrM 2397 A A 25 0 25 1 , I -chrM 2398 G G 25 0 25 1 , I -chrM 2399 C C 25 0 25 1 , I -chrM 2400 G G 25 0 25 1 , I -chrM 2401 C C 25 0 25 1 , I -chrM 2402 A A 25 0 25 1 , I -chrM 2403 A A 25 0 25 1 , I -chrM 2404 T T 25 0 25 1 , I -chrM 2405 C C 25 0 25 1 , I -chrM 2406 C C 25 0 25 1 , I -chrM 2407 T T 25 0 25 1 , G -chrM 2408 A A 25 0 25 1 , I -chrM 2409 T T 25 0 25 1 , I -chrM 2410 T T 25 0 25 1 , B -chrM 2411 C C 25 0 25 1 , I -chrM 2412 C C 25 0 25 1 , I -chrM 2413 A A 25 0 25 1 , I -chrM 2414 G G 25 0 25 1 , I -chrM 2415 A A 25 0 25 1 , I -chrM 2416 G A 4 4 25 1 n " -chrM 2417 T A 4 4 25 1 n " -chrM 2418 C C 25 0 25 1 , I -chrM 2419 C C 25 0 25 1 , I -chrM 2420 A A 25 0 25 1 , I -chrM 2421 T T 25 0 25 1 , I -chrM 2422 A A 25 0 25 1 , I -chrM 2423 T T 25 0 25 1 , I -chrM 2424 C C 25 0 25 1 ,$ I -chrM 2735 t T 25 0 25 1 ^:, I -chrM 2736 t T 24 0 25 1 , 9 -chrM 2737 t T 25 0 25 1 , I -chrM 2738 a A 25 0 25 1 , I -chrM 2739 c C 25 0 25 1 , I -chrM 2740 a A 25 0 25 1 , I -chrM 2741 c C 25 0 25 1 , I -chrM 2742 t T 20 0 25 1 , 5 -chrM 2743 c C 25 0 25 1 , I -chrM 2744 a A 25 0 25 1 , I -chrM 2745 g G 25 0 25 1 , I -chrM 2746 a A 25 0 25 1 , I -chrM 2747 g G 25 0 25 1 , I -chrM 2748 g G 25 0 25 1 , I -chrM 2749 t T 25 0 25 1 , I -chrM 2750 t T 25 0 25 1 , I -chrM 2751 c C 25 0 25 1 , I -chrM 2752 a A 25 0 25 1 , I -chrM 2753 a A 25 0 25 1 , I -chrM 2754 c C 25 0 25 1 , I -chrM 2755 t T 25 0 25 1 , I -chrM 2756 c C 25 0 25 1 , I -chrM 2757 c C 25 0 25 1 , I -chrM 2758 t T 25 0 25 1 , I -chrM 2759 c C 25 0 25 1 , I -chrM 2760 t T 25 0 25 1 , I -chrM 2761 c C 25 0 25 1 , I -chrM 2762 c A 4 4 25 1 n " -chrM 2763 c A 4 4 25 1 n " -chrM 2764 t T 25 0 25 1 , I -chrM 2765 a A 25 0 25 1 , I -chrM 2766 a A 25 0 25 1 , I -chrM 2767 c C 25 0 25 1 , I -chrM 2768 a A 25 0 25 1 , I -chrM 2769 a A 25 0 25 1 , I -chrM 2770 c C 25 0 25 1 ,$ I -chrM 2844 G G 25 0 25 1 ^:. I -chrM 2845 A A 25 0 25 1 . I -chrM 2846 A A 25 0 25 1 . I -chrM 2847 A A 25 0 25 1 . I -chrM 2848 A A 25 0 25 1 . I -chrM 2849 G G 25 0 25 1 . I -chrM 2850 T T 25 0 25 1 . I -chrM 2851 C A 4 4 25 1 N " -chrM 2852 T A 4 4 25 1 N " -chrM 2853 T T 25 0 25 1 . I -chrM 2854 A A 25 0 25 1 . I -chrM 2855 G G 25 0 25 1 . I -chrM 2856 G G 25 0 25 1 . I -chrM 2857 C C 25 0 25 1 . I -chrM 2858 T T 25 0 25 1 . I -chrM 2859 A A 25 0 25 1 . I -chrM 2860 T T 25 0 25 1 . I -chrM 2861 A A 25 0 25 1 . B -chrM 2862 T T 25 0 25 1 . I -chrM 2863 G G 25 0 25 1 . I -chrM 2864 C C 25 0 25 1 . I -chrM 2865 A A 25 0 25 1 . I -chrM 2866 A A 25 0 25 1 . B -chrM 2867 C C 25 0 25 1 . I -chrM 2868 T T 25 0 25 1 . I -chrM 2869 T T 25 0 25 1 . I -chrM 2870 C C 25 0 25 1 . I -chrM 2871 G G 25 0 25 1 . = -chrM 2872 C C 25 0 25 1 . I -chrM 2873 A A 25 0 25 1 . @ -chrM 2874 A A 24 0 25 1 . 9 -chrM 2875 A A 21 0 25 1 . 6 -chrM 2876 G G 25 0 25 1 . D -chrM 2877 G G 17 0 25 1 . 2 -chrM 2878 A A 9 0 25 1 . * -chrM 2879 C C 25 0 25 1 .$ I -chrM 3080 T T 25 0 25 1 ^:. I -chrM 3081 T T 25 0 25 1 . I -chrM 3082 C C 25 0 25 1 . I -chrM 3083 A A 25 0 25 1 . I -chrM 3084 T T 25 0 25 1 . I -chrM 3085 A A 25 0 25 1 . I -chrM 3086 C C 25 0 25 1 . I -chrM 3087 T A 4 4 25 1 N " -chrM 3088 A A 4 0 25 1 N " -chrM 3089 G G 25 0 25 1 . I -chrM 3090 C C 25 0 25 1 . I -chrM 3091 C C 25 0 25 1 . I -chrM 3092 A A 25 0 25 1 . I -chrM 3093 T T 25 0 25 1 . I -chrM 3094 G G 25 0 25 1 . I -chrM 3095 T T 25 0 25 1 . I -chrM 3096 C C 25 0 25 1 . I -chrM 3097 C C 25 0 25 1 . I -chrM 3098 A A 25 0 25 1 . I -chrM 3099 G G 25 0 25 1 . H -chrM 3100 C C 25 0 25 1 . I -chrM 3101 C C 25 0 25 1 . I -chrM 3102 T T 25 0 25 1 . I -chrM 3103 A A 25 0 25 1 . I -chrM 3104 G G 25 0 25 1 . I -chrM 3105 C C 25 0 25 1 . I -chrM 3106 T T 25 0 25 1 . I -chrM 3107 G G 25 0 25 1 . I -chrM 3108 T T 25 0 25 1 . I -chrM 3109 C C 25 0 25 1 . I -chrM 3110 T T 25 0 25 1 . I -chrM 3111 A A 25 0 25 1 . < -chrM 3112 C C 25 0 25 1 . I -chrM 3113 T T 25 0 25 1 . I -chrM 3114 C C 25 0 25 1 . I -chrM 3115 A A 25 0 25 1 .$ F -chrM 3188 A A 25 0 25 1 ^:, I -chrM 3189 T T 25 0 25 1 , = -chrM 3190 C C 25 0 25 1 , I -chrM 3191 T T 25 0 25 1 , I -chrM 3192 C C 25 0 25 1 , I -chrM 3193 A A 25 0 25 1 , I -chrM 3194 T T 25 0 25 1 , I -chrM 3195 A A 25 0 25 1 , I -chrM 3196 C C 25 0 25 1 , I -chrM 3197 G G 25 0 25 1 , @ -chrM 3198 A A 25 0 25 1 , I -chrM 3199 A A 25 0 25 1 , I -chrM 3200 G G 25 0 25 1 , I -chrM 3201 T T 25 0 25 1 , I -chrM 3202 A A 25 0 25 1 , I -chrM 3203 A A 25 0 25 1 , I -chrM 3204 C C 25 0 25 1 , I -chrM 3205 T T 25 0 25 1 , I -chrM 3206 C C 25 0 25 1 , I -chrM 3207 T T 25 0 25 1 , I -chrM 3208 A A 25 0 25 1 , I -chrM 3209 G G 25 0 25 1 , I -chrM 3210 C C 25 0 25 1 , I -chrM 3211 A A 25 0 25 1 , I -chrM 3212 A A 25 0 25 1 , I -chrM 3213 T T 25 0 25 1 , I -chrM 3214 C C 25 0 25 1 , I -chrM 3215 A A 4 0 25 1 n " -chrM 3216 T A 4 4 25 1 n " -chrM 3217 C C 25 0 25 1 , I -chrM 3218 C C 25 0 25 1 , I -chrM 3219 T T 25 0 25 1 , I -chrM 3220 A A 25 0 25 1 , I -chrM 3221 C C 25 0 25 1 , I -chrM 3222 T T 25 0 25 1 , I -chrM 3223 C C 25 0 25 1 ,$ I -chrM 3502 A A 25 0 25 1 ^:. I -chrM 3503 G G 25 0 25 1 . I -chrM 3504 C C 25 0 25 1 . I -chrM 3505 A A 25 0 25 1 . I -chrM 3506 T T 25 0 25 1 . I -chrM 3507 T T 25 0 25 1 . I -chrM 3508 T T 25 0 25 1 . I -chrM 3509 C A 4 4 25 1 N " -chrM 3510 A A 4 0 25 1 N " -chrM 3511 C C 25 0 25 1 . I -chrM 3512 A A 25 0 25 1 . I -chrM 3513 A A 25 0 25 1 . I -chrM 3514 C C 25 0 25 1 . I -chrM 3515 C C 25 0 25 1 . I -chrM 3516 C C 25 0 25 1 . I -chrM 3517 C C 25 0 25 1 . I -chrM 3518 T T 25 0 25 1 . I -chrM 3519 A A 25 0 25 1 . I -chrM 3520 C C 25 0 25 1 . I -chrM 3521 C C 25 0 25 1 . I -chrM 3522 T T 25 0 25 1 . I -chrM 3523 G G 25 0 25 1 . I -chrM 3524 C C 25 0 25 1 . I -chrM 3525 C C 25 0 25 1 . I -chrM 3526 A A 25 0 25 1 . > -chrM 3527 G G 25 0 25 1 . I -chrM 3528 A A 19 0 25 1 . 4 -chrM 3529 A A 25 0 25 1 . @ -chrM 3530 C C 25 0 25 1 . I -chrM 3531 T T 25 0 25 1 . I -chrM 3532 C C 25 0 25 1 . I -chrM 3533 T T 25 0 25 1 . I -chrM 3534 A A 25 0 25 1 . I -chrM 3535 C C 25 0 25 1 . I -chrM 3536 T T 25 0 25 1 . I -chrM 3537 C C 25 0 25 1 .$ I -chrM 3678 G G 25 0 25 1 ^:. I -chrM 3679 A A 25 0 25 1 . I -chrM 3680 C C 25 0 25 1 . I -chrM 3681 A A 25 0 25 1 . I -chrM 3682 C C 25 0 25 1 . I -chrM 3683 G G 25 0 25 1 . I -chrM 3684 T T 25 0 25 1 . I -chrM 3685 C A 4 4 25 1 N " -chrM 3686 T A 4 4 25 1 N " -chrM 3687 C C 25 0 25 1 . I -chrM 3688 A A 25 0 25 1 . I -chrM 3689 C C 25 0 25 1 . I -chrM 3690 T T 25 0 25 1 . I -chrM 3691 T T 25 0 25 1 . I -chrM 3692 C C 25 0 25 1 . I -chrM 3693 C C 25 0 25 1 . I -chrM 3694 A A 25 0 25 1 . I -chrM 3695 A A 25 0 25 1 . : -chrM 3696 T T 25 0 25 1 . I -chrM 3697 C C 25 0 25 1 . I -chrM 3698 A A 25 0 25 1 . I -chrM 3699 T T 25 0 25 1 . I -chrM 3700 A A 23 0 25 1 . 8 -chrM 3701 C C 25 0 25 1 . I -chrM 3702 T T 25 0 25 1 . I -chrM 3703 A A 25 0 25 1 . E -chrM 3704 T T 25 0 25 1 . I -chrM 3705 C C 25 0 25 1 . I -chrM 3706 C C 25 0 25 1 . I -chrM 3707 A A 25 0 25 1 . I -chrM 3708 G G 12 0 25 1 . - -chrM 3709 C C 25 0 25 1 . I -chrM 3710 A A 25 0 25 1 . A -chrM 3711 T T 25 0 25 1 . I -chrM 3712 C C 25 0 25 1 . I -chrM 3713 C C 25 0 25 1 .$ I -chrM 3753 T T 25 0 25 1 ^:. I -chrM 3754 T T 25 0 25 1 . I -chrM 3755 T T 25 0 25 1 . I -chrM 3756 G G 25 0 25 1 . I -chrM 3757 A A 25 0 25 1 . I -chrM 3758 T T 25 0 25 1 . I -chrM 3759 A A 25 0 25 1 . I -chrM 3760 G A 4 4 25 1 N " -chrM 3761 A A 4 0 25 1 N " -chrM 3762 G G 25 0 25 1 . I -chrM 3763 T T 25 0 25 1 . I -chrM 3764 A A 25 0 25 1 . I -chrM 3765 A A 25 0 25 1 . I -chrM 3766 A A 25 0 25 1 . I -chrM 3767 A A 25 0 25 1 . I -chrM 3768 C C 25 0 25 1 . I -chrM 3769 A A 25 0 25 1 . I -chrM 3770 T T 25 0 25 1 . I -chrM 3771 A A 25 0 25 1 . I -chrM 3772 G G 25 0 25 1 . I -chrM 3773 A A 25 0 25 1 . I -chrM 3774 G G 25 0 25 1 . I -chrM 3775 G G 25 0 25 1 . I -chrM 3776 C C 25 0 25 1 . I -chrM 3777 T T 25 0 25 1 . I -chrM 3778 C C 25 0 25 1 . I -chrM 3779 A A 25 0 25 1 . C -chrM 3780 A A 25 0 25 1 . I -chrM 3781 A A 25 0 25 1 . I -chrM 3782 C C 25 0 25 1 . I -chrM 3783 C C 25 0 25 1 . I -chrM 3784 C C 25 0 25 1 . I -chrM 3785 T T 25 0 25 1 . I -chrM 3786 C C 25 0 25 1 . I -chrM 3787 T T 25 0 25 1 . I -chrM 3788 T T 25 0 25 1 .$ I -chrM 3841 t T 25 0 25 1 ^:, G -chrM 3842 g G 25 0 25 1 , I -chrM 3843 c C 10 0 25 1 , + -chrM 3844 t T 25 0 25 1 , I -chrM 3845 a A 25 0 25 1 , I -chrM 3846 c C 4 0 25 1 , % -chrM 3847 c C 7 0 25 1 , ( -chrM 3848 g G 25 0 25 1 , I -chrM 3849 a A 25 0 25 1 , I -chrM 3850 a A 25 0 25 1 , I -chrM 3851 t T 25 0 25 1 , I -chrM 3852 t T 25 0 25 1 , I -chrM 3853 a A 25 0 25 1 , I -chrM 3854 c C 25 0 25 1 , I -chrM 3855 a A 25 0 25 1 , I -chrM 3856 c C 25 0 25 1 , I -chrM 3857 c C 25 0 25 1 , I -chrM 3858 a A 25 0 25 1 , I -chrM 3859 t T 25 0 25 1 , I -chrM 3860 g G 25 0 25 1 , I -chrM 3861 t T 25 0 25 1 , I -chrM 3862 c C 25 0 25 1 , I -chrM 3863 c C 25 0 25 1 , I -chrM 3864 t T 25 0 25 1 , I -chrM 3865 a A 25 0 25 1 , I -chrM 3866 C C 25 0 25 1 , I -chrM 3867 A A 25 0 25 1 , I -chrM 3868 A A 4 0 25 1 n " -chrM 3869 G A 4 4 25 1 n " -chrM 3870 T T 25 0 25 1 , I -chrM 3871 A A 25 0 25 1 , I -chrM 3872 A A 25 0 25 1 , I -chrM 3873 G G 25 0 25 1 , I -chrM 3874 G G 25 0 25 1 , I -chrM 3875 T T 25 0 25 1 , I -chrM 3876 C C 25 0 25 1 ,$ I -chrM 3921 C C 25 0 25 1 ^:, I -chrM 3922 A A 25 0 25 1 , I -chrM 3923 C C 25 0 25 1 , I -chrM 3924 C C 25 0 25 1 , I -chrM 3925 C C 25 0 25 1 , I -chrM 3926 T T 25 0 25 1 , = -chrM 3927 T T 25 0 25 1 , A -chrM 3928 C C 25 0 25 1 , I -chrM 3929 C C 25 0 25 1 , I -chrM 3930 C C 25 0 25 1 , I -chrM 3931 G G 25 0 25 1 , I -chrM 3932 T T 25 0 25 1 , I -chrM 3933 A A 25 0 25 1 , I -chrM 3934 C C 25 0 25 1 , I -chrM 3935 T T 25 0 25 1 , I -chrM 3936 A A 25 0 25 1 , I -chrM 3937 A A 25 0 25 1 , I -chrM 3938 T T 25 0 25 1 , I -chrM 3939 A A 25 0 25 1 , I -chrM 3940 A A 25 0 25 1 , I -chrM 3941 A A 25 0 25 1 , I -chrM 3942 T T 25 0 25 1 , B -chrM 3943 C C 25 0 25 1 , I -chrM 3944 C C 25 0 25 1 , I -chrM 3945 C C 25 0 25 1 , I -chrM 3946 C C 25 0 25 1 , I -chrM 3947 T T 25 0 25 1 , I -chrM 3948 T A 4 4 25 1 n " -chrM 3949 A A 4 0 25 1 n " -chrM 3950 T T 25 0 25 1 , I -chrM 3951 C C 25 0 25 1 , I -chrM 3952 T T 25 0 25 1 , I -chrM 3953 T T 25 0 25 1 , I -chrM 3954 C C 25 0 25 1 , I -chrM 3955 A A 25 0 25 1 , I -chrM 3956 C C 25 0 25 1 ,$ I -chrM 4249 A A 25 0 25 1 ^:, I -chrM 4250 A A 25 0 25 1 , I -chrM 4251 A A 25 0 25 1 , I -chrM 4252 C C 25 0 25 1 , I -chrM 4253 T T 20 0 25 1 , 5 -chrM 4254 T T 21 0 25 1 , 6 -chrM 4255 G G 25 0 25 1 , I -chrM 4256 G G 25 0 25 1 , I -chrM 4257 A A 25 0 25 1 , I -chrM 4258 C C 25 0 25 1 , I -chrM 4259 T T 25 0 25 1 , I -chrM 4260 C C 25 0 25 1 , I -chrM 4261 A A 25 0 25 1 , I -chrM 4262 C C 25 0 25 1 , I -chrM 4263 A A 25 0 25 1 , I -chrM 4264 C C 25 0 25 1 , I -chrM 4265 C C 25 0 25 1 , I -chrM 4266 A A 25 0 25 1 , I -chrM 4267 T T 25 0 25 1 , I -chrM 4268 T T 25 0 25 1 , I -chrM 4269 C C 25 0 25 1 , I -chrM 4270 C C 25 0 25 1 , I -chrM 4271 A A 25 0 25 1 , I -chrM 4272 C C 25 0 25 1 , I -chrM 4273 T T 25 0 25 1 , I -chrM 4274 T T 25 0 25 1 , I -chrM 4275 C C 25 0 25 1 , I -chrM 4276 T A 4 4 25 1 n " -chrM 4277 G A 4 4 25 1 n " -chrM 4278 A A 25 0 25 1 , I -chrM 4279 G G 25 0 25 1 , I -chrM 4280 T T 25 0 25 1 , I -chrM 4281 A A 25 0 25 1 , I -chrM 4282 C C 25 0 25 1 , I -chrM 4283 C C 25 0 25 1 , I -chrM 4284 C C 25 0 25 1 ,$ I -chrM 4552 T T 25 0 25 1 ^:. I -chrM 4553 T T 25 0 25 1 . I -chrM 4554 A A 25 0 25 1 . I -chrM 4555 A A 25 0 25 1 . I -chrM 4556 T T 25 0 25 1 . I -chrM 4557 T T 25 0 25 1 . I -chrM 4558 T T 25 0 25 1 . I -chrM 4559 A A 4 0 25 1 N " -chrM 4560 C A 4 4 25 1 N " -chrM 4561 A A 25 0 25 1 . I -chrM 4562 T T 25 0 25 1 . I -chrM 4563 T T 25 0 25 1 . I -chrM 4564 A A 25 0 25 1 . I -chrM 4565 T T 25 0 25 1 . I -chrM 4566 A A 25 0 25 1 . I -chrM 4567 A A 25 0 25 1 . I -chrM 4568 T T 25 0 25 1 . I -chrM 4569 A A 25 0 25 1 . I -chrM 4570 A A 25 0 25 1 . I -chrM 4571 C C 25 0 25 1 . I -chrM 4572 A A 25 0 25 1 . I -chrM 4573 C C 25 0 25 1 . I -chrM 4574 T T 25 0 25 1 . I -chrM 4575 C C 25 0 25 1 . I -chrM 4576 A A 25 0 25 1 . I -chrM 4577 C C 25 0 25 1 . I -chrM 4578 A A 25 0 25 1 . I -chrM 4579 A A 25 0 25 1 . ? -chrM 4580 T T 25 0 25 1 . I -chrM 4581 A A 21 0 25 1 . 6 -chrM 4582 T T 25 0 25 1 . I -chrM 4583 T T 25 0 25 1 . I -chrM 4584 C C 25 0 25 1 . I -chrM 4585 A A 25 0 25 1 . I -chrM 4586 T T 25 0 25 1 . I -chrM 4587 A A 21 0 25 1 .$ 6 -chrM 4697 T T 20 0 25 1 ^:, 5 -chrM 4698 C C 25 0 25 1 , = -chrM 4699 C C 19 0 25 1 , 4 -chrM 4700 C C 5 0 25 1 , & -chrM 4701 C C 25 0 25 1 , G -chrM 4702 C C 16 0 25 1 , 1 -chrM 4703 C C 18 0 25 1 , 3 -chrM 4704 A A 25 0 25 1 , I -chrM 4705 C C 13 0 25 1 , . -chrM 4706 T T 25 0 25 1 , ? -chrM 4707 A A 25 0 25 1 , I -chrM 4708 T T 25 0 25 1 , I -chrM 4709 C C 25 0 25 1 , I -chrM 4710 A A 25 0 25 1 , I -chrM 4711 G G 25 0 25 1 , I -chrM 4712 G G 25 0 25 1 , I -chrM 4713 A A 25 0 25 1 , I -chrM 4714 T T 25 0 25 1 , I -chrM 4715 T T 25 0 25 1 , I -chrM 4716 C C 25 0 25 1 , I -chrM 4717 A A 25 0 25 1 , I -chrM 4718 T T 25 0 25 1 , I -chrM 4719 A A 25 0 25 1 , I -chrM 4720 C C 25 0 25 1 , I -chrM 4721 C C 25 0 25 1 , I -chrM 4722 C C 25 0 25 1 , I -chrM 4723 A A 25 0 25 1 , I -chrM 4724 A A 4 0 25 1 n " -chrM 4725 A A 4 0 25 1 n " -chrM 4726 T T 25 0 25 1 , I -chrM 4727 G G 25 0 25 1 , I -chrM 4728 A A 25 0 25 1 , I -chrM 4729 A A 25 0 25 1 , I -chrM 4730 T T 25 0 25 1 , I -chrM 4731 A A 25 0 25 1 , I -chrM 4732 A A 25 0 25 1 ,$ I -chrM 4742 A A 25 0 25 1 ^:. I -chrM 4743 G G 25 0 25 1 . I -chrM 4744 C C 25 0 25 1 . I -chrM 4745 T T 25 0 25 1 . I -chrM 4746 C C 25 0 25 1 . I -chrM 4747 A A 25 0 25 1 . I -chrM 4748 C C 25 0 25 1 . I -chrM 4749 C A 4 4 25 1 N " -chrM 4750 A A 4 0 25 1 N " -chrM 4751 A A 25 0 25 1 . I -chrM 4752 A A 25 0 25 1 . I -chrM 4753 A A 25 0 25 1 . I -chrM 4754 A A 25 0 25 1 . I -chrM 4755 T T 25 0 25 1 . I -chrM 4756 A A 25 0 25 1 . I -chrM 4757 G G 25 0 25 1 . I -chrM 4758 C C 25 0 25 1 . I -chrM 4759 A A 25 0 25 1 . I -chrM 4760 G G 25 0 25 1 . I -chrM 4761 C C 25 0 25 1 . I -chrM 4762 A A 25 0 25 1 . I -chrM 4763 T T 25 0 25 1 . I -chrM 4764 C C 25 0 25 1 . I -chrM 4765 A A 25 0 25 1 . I -chrM 4766 T T 25 0 25 1 . I -chrM 4767 C C 25 0 25 1 . I -chrM 4768 C C 25 0 25 1 . I -chrM 4769 T T 25 0 25 1 . I -chrM 4770 C C 25 0 25 1 . I -chrM 4771 C C 25 0 25 1 . I -chrM 4772 C C 25 0 25 1 . I -chrM 4773 C C 25 0 25 1 . I -chrM 4774 A A 23 0 25 1 . 8 -chrM 4775 C C 25 0 25 1 . I -chrM 4776 A A 25 0 25 1 . : -chrM 4777 C C 25 0 25 1 .$ I -chrM 4932 C C 25 0 25 1 ^:, I -chrM 4933 T T 12 0 25 1 , - -chrM 4934 C C 25 0 25 1 , A -chrM 4935 C C 25 0 25 1 , I -chrM 4936 C C 25 0 25 1 , I -chrM 4937 T T 22 0 25 1 , 7 -chrM 4938 A A 25 0 25 1 , I -chrM 4939 C C 25 0 25 1 , I -chrM 4940 T T 20 0 25 1 , 5 -chrM 4941 C C 25 0 25 1 , I -chrM 4942 C C 25 0 25 1 , I -chrM 4943 T T 25 0 25 1 , : -chrM 4944 C C 25 0 25 1 , I -chrM 4945 C C 25 0 25 1 , I -chrM 4946 C C 25 0 25 1 , I -chrM 4947 C C 25 0 25 1 , I -chrM 4948 C C 25 0 25 1 , I -chrM 4949 T T 25 0 25 1 , I -chrM 4950 A A 25 0 25 1 , I -chrM 4951 A A 25 0 25 1 , I -chrM 4952 C C 25 0 25 1 , I -chrM 4953 C C 25 0 25 1 , I -chrM 4954 C C 25 0 25 1 , I -chrM 4955 C C 25 0 25 1 , I -chrM 4956 C C 25 0 25 1 , I -chrM 4957 A A 25 0 25 1 , I -chrM 4958 T T 25 0 25 1 , I -chrM 4959 A A 4 0 25 1 n " -chrM 4960 C A 4 4 25 1 n " -chrM 4961 T T 25 0 25 1 , I -chrM 4962 A A 25 0 25 1 , I -chrM 4963 T T 25 0 25 1 , I -chrM 4964 C C 25 0 25 1 , I -chrM 4965 A A 25 0 25 1 , I -chrM 4966 A A 25 0 25 1 , I -chrM 4967 T T 25 0 25 1 ,$ I -chrM 5155 G G 22 0 25 1 ^:, 7 -chrM 5156 T T 25 0 25 1 , I -chrM 5157 T T 25 0 25 1 , I -chrM 5158 A A 25 0 25 1 , I -chrM 5159 A A 25 0 25 1 , I -chrM 5160 C C 25 0 25 1 , I -chrM 5161 A A 25 0 25 1 , I -chrM 5162 G G 25 0 25 1 , I -chrM 5163 C C 25 0 25 1 , I -chrM 5164 T T 25 0 25 1 , I -chrM 5165 A A 25 0 25 1 , I -chrM 5166 A A 25 0 25 1 , I -chrM 5167 A A 25 0 25 1 , I -chrM 5168 T T 25 0 25 1 , I -chrM 5169 A A 25 0 25 1 , I -chrM 5170 C C 25 0 25 1 , I -chrM 5171 C C 25 0 25 1 , I -chrM 5172 C C 25 0 25 1 , I -chrM 5173 T T 25 0 25 1 , I -chrM 5174 A A 25 0 25 1 , I -chrM 5175 A A 25 0 25 1 , I -chrM 5176 T T 25 0 25 1 , I -chrM 5177 C C 25 0 25 1 , I -chrM 5178 A A 25 0 25 1 , I -chrM 5179 A A 25 0 25 1 , I -chrM 5180 C C 25 0 25 1 , I -chrM 5181 T T 25 0 25 1 , I -chrM 5182 G A 4 4 25 1 n " -chrM 5183 G A 4 4 25 1 n " -chrM 5184 C C 25 0 25 1 , I -chrM 5185 T T 25 0 25 1 , I -chrM 5186 T T 25 0 25 1 , I -chrM 5187 C C 25 0 25 1 , I -chrM 5188 A A 25 0 25 1 , I -chrM 5189 A A 25 0 25 1 , I -chrM 5190 T T 25 0 25 1 ,$ I -chrM 5309 T T 25 0 25 1 ^:, I -chrM 5310 C C 25 0 25 1 , I -chrM 5311 C C 25 0 25 1 , I -chrM 5312 A A 25 0 25 1 , I -chrM 5313 A A 25 0 25 1 , I -chrM 5314 C C 25 0 25 1 , I -chrM 5315 C C 25 0 25 1 , I -chrM 5316 C C 25 0 25 1 , I -chrM 5317 C C 25 0 25 1 , I -chrM 5318 T T 25 0 25 1 , I -chrM 5319 G G 25 0 25 1 , I -chrM 5320 T T 25 0 25 1 , I -chrM 5321 C C 25 0 25 1 , I -chrM 5322 T T 25 0 25 1 , I -chrM 5323 T T 25 0 25 1 , I -chrM 5324 T T 25 0 25 1 , I -chrM 5325 A A 25 0 25 1 , I -chrM 5326 G G 25 0 25 1 , I -chrM 5327 A A 25 0 25 1 , I -chrM 5328 T T 25 0 25 1 , I -chrM 5329 T T 25 0 25 1 , I -chrM 5330 T T 25 0 25 1 , I -chrM 5331 A A 25 0 25 1 , I -chrM 5332 C C 25 0 25 1 , I -chrM 5333 A A 25 0 25 1 , I -chrM 5334 G G 25 0 25 1 , I -chrM 5335 T T 25 0 25 1 , I -chrM 5336 C A 4 4 25 1 n " -chrM 5337 T A 4 4 25 1 n " -chrM 5338 A A 25 0 25 1 , I -chrM 5339 A A 25 0 25 1 , I -chrM 5340 T T 25 0 25 1 , I -chrM 5341 G G 25 0 25 1 , I -chrM 5342 C C 25 0 25 1 , I -chrM 5343 T T 25 0 25 1 , I -chrM 5344 T T 25 0 25 1 ,$ I -chrM 5540 C C 25 0 25 1 ^:, ? -chrM 5541 C C 25 0 25 1 , : -chrM 5542 C C 25 0 25 1 , ; -chrM 5543 A A 25 0 25 1 , I -chrM 5544 T T 24 0 25 1 , 9 -chrM 5545 G G 25 0 25 1 , D -chrM 5546 C C 25 0 25 1 , D -chrM 5547 A A 25 0 25 1 , I -chrM 5548 T T 25 0 25 1 , B -chrM 5549 T T 25 0 25 1 , E -chrM 5550 C C 25 0 25 1 , I -chrM 5551 G G 25 0 25 1 , I -chrM 5552 T T 25 0 25 1 , I -chrM 5553 A A 25 0 25 1 , I -chrM 5554 A A 25 0 25 1 , I -chrM 5555 T T 25 0 25 1 , I -chrM 5556 A A 25 0 25 1 , I -chrM 5557 A A 25 0 25 1 , I -chrM 5558 T T 25 0 25 1 , E -chrM 5559 T T 25 0 25 1 , I -chrM 5560 T T 25 0 25 1 , E -chrM 5561 T T 25 0 25 1 , I -chrM 5562 C C 25 0 25 1 , I -chrM 5563 T T 25 0 25 1 , I -chrM 5564 T T 25 0 25 1 , I -chrM 5565 T T 25 0 25 1 , I -chrM 5566 A A 25 0 25 1 , I -chrM 5567 T A 4 4 25 1 n " -chrM 5568 G A 4 4 25 1 n " -chrM 5569 G G 25 0 25 1 , I -chrM 5570 T T 25 0 25 1 , I -chrM 5571 C C 25 0 25 1 , I -chrM 5572 A A 25 0 25 1 , I -chrM 5573 T T 25 0 25 1 , I -chrM 5574 A A 25 0 25 1 , I -chrM 5575 C C 25 0 25 1 ,$ I -chrM 6016 T T 25 0 25 1 ^:, @ -chrM 6017 T T 22 0 25 1 , 7 -chrM 6018 C C 25 0 25 1 , I -chrM 6019 T T 25 0 25 1 , < -chrM 6020 T T 25 0 25 1 , ? -chrM 6021 C C 25 0 25 1 , I -chrM 6022 G G 25 0 25 1 , I -chrM 6023 A A 25 0 25 1 , I -chrM 6024 C C 25 0 25 1 , I -chrM 6025 C C 25 0 25 1 , I -chrM 6026 C C 25 0 25 1 , I -chrM 6027 C C 25 0 25 1 , I -chrM 6028 G G 25 0 25 1 , I -chrM 6029 C C 25 0 25 1 , I -chrM 6030 A A 25 0 25 1 , I -chrM 6031 G G 25 0 25 1 , I -chrM 6032 G G 25 0 25 1 , I -chrM 6033 A A 25 0 25 1 , I -chrM 6034 G G 25 0 25 1 , I -chrM 6035 G G 25 0 25 1 , I -chrM 6036 A A 25 0 25 1 , I -chrM 6037 G G 25 0 25 1 , I -chrM 6038 G G 25 0 25 1 , I -chrM 6039 G G 25 0 25 1 , I -chrM 6040 G G 33 0 25 2 ,^:. II +chrM 1534 T T 33 0 25 2 ,$, >I +chrM 1535 T T 30 0 25 1 , I +chrM 1536 T T 30 0 25 1 , I +chrM 1537 A A 30 0 25 1 , > +chrM 1538 A A 30 0 25 1 ,$ ; +chrM 1616 A A 30 0 25 1 ^:. E +chrM 1617 G G 30 0 25 1 . I +chrM 1618 T T 30 0 25 1 . I +chrM 1619 T T 30 0 25 1 . I +chrM 1620 G G 30 0 25 1 . I +chrM 1621 G G 30 0 25 1 . I +chrM 1622 C C 30 0 25 1 . I +chrM 1623 T N 0 0 0 1 N " +chrM 1624 T N 0 0 0 1 N " +chrM 1625 A A 30 0 25 1 . I +chrM 1626 A A 30 0 25 1 . I +chrM 1627 A A 30 0 25 1 . I +chrM 1628 A A 30 0 25 1 . I +chrM 1629 G G 30 0 25 1 . I +chrM 1630 C C 30 0 25 1 . I +chrM 1631 A A 30 0 25 1 . I +chrM 1632 G G 30 0 25 1 . I +chrM 1633 C C 30 0 25 1 . I +chrM 1634 C C 30 0 25 1 . I +chrM 1635 A A 30 0 25 1 . C +chrM 1636 T T 30 0 25 1 . I +chrM 1637 C C 30 0 25 1 . I +chrM 1638 A A 30 0 25 1 . = +chrM 1639 A A 30 0 25 1 . G +chrM 1640 T T 30 0 25 1 . I +chrM 1641 T T 30 0 25 1 . I +chrM 1642 A A 30 0 25 1 . I +chrM 1643 A A 30 0 25 1 . I +chrM 1644 G G 30 0 25 1 . I +chrM 1645 A A 30 0 25 1 . @ +chrM 1646 A A 30 0 25 1 . I +chrM 1647 A A 30 0 25 1 . G +chrM 1648 G G 30 0 25 1 . I +chrM 1649 C C 30 0 25 1 . I +chrM 1650 G G 30 0 25 1 . I +chrM 1651 T T 30 0 25 1 .$ > +chrM 2261 C C 30 0 25 1 ^:, E +chrM 2262 A A 30 0 25 1 , I +chrM 2263 G G 30 0 25 1 , I +chrM 2264 C C 30 0 25 1 , I +chrM 2265 A A 30 0 25 1 , G +chrM 2266 A A 30 0 25 1 , I +chrM 2267 T T 30 0 25 1 , 2 +chrM 2268 T T 30 0 25 1 , = +chrM 2269 T T 30 0 25 1 , 3 +chrM 2270 C C 30 0 25 1 , I +chrM 2271 G G 30 0 25 1 , I +chrM 2272 G G 30 0 25 1 , I +chrM 2273 T T 30 0 25 1 , I +chrM 2274 T T 30 0 25 1 , I +chrM 2275 G G 30 0 25 1 , I +chrM 2276 G G 30 0 25 1 , I +chrM 2277 G G 30 0 25 1 , I +chrM 2278 G G 30 0 25 1 , I +chrM 2279 T T 30 0 25 1 , I +chrM 2280 G G 30 0 25 1 , I +chrM 2281 A A 30 0 25 1 , I +chrM 2282 C C 30 0 25 1 , I +chrM 2283 C C 30 0 25 1 , I +chrM 2284 T T 30 0 25 1 , I +chrM 2285 C C 30 0 25 1 , I +chrM 2286 G G 30 0 25 1 , I +chrM 2287 G G 30 0 25 1 , I +chrM 2288 A N 0 0 0 1 n " +chrM 2289 G N 0 0 0 1 n " +chrM 2290 A A 30 0 25 1 , I +chrM 2291 A A 30 0 25 1 , I +chrM 2292 C C 30 0 25 1 , I +chrM 2293 A A 30 0 25 1 , E +chrM 2294 A A 30 0 25 1 , B +chrM 2295 A A 30 0 25 1 , @ +chrM 2296 A A 30 0 25 1 ,$ ? +chrM 2334 A A 30 0 25 1 ^:, ; +chrM 2335 A A 30 0 25 1 , ; +chrM 2336 A A 30 0 25 1 , > +chrM 2337 T T 30 0 25 1 , I +chrM 2338 A A 30 0 25 1 , I +chrM 2339 T T 30 0 25 1 , H +chrM 2340 A A 30 0 25 1 , I +chrM 2341 T T 30 0 25 1 , = +chrM 2342 A A 30 0 25 1 , I +chrM 2343 A A 30 0 25 1 , I +chrM 2344 T T 30 0 25 1 , C +chrM 2345 C C 30 0 25 1 , I +chrM 2346 A A 30 0 25 1 , I +chrM 2347 C C 30 0 25 1 , I +chrM 2348 T T 30 0 25 1 , ? +chrM 2349 T T 30 0 25 1 , I +chrM 2350 A A 30 0 25 1 , I +chrM 2351 T T 30 0 25 1 , I +chrM 2352 T T 30 0 25 1 , I +chrM 2353 G G 30 0 25 1 , I +chrM 2354 A A 30 0 25 1 , I +chrM 2355 T T 30 0 25 1 , D +chrM 2356 C C 30 0 25 1 , I +chrM 2357 C C 30 0 25 1 , I +chrM 2358 A A 30 0 25 1 , I +chrM 2359 A A 30 0 25 1 , I +chrM 2360 A A 30 0 25 1 , I +chrM 2361 C N 0 0 0 1 n " +chrM 2362 C N 0 0 0 1 n " +chrM 2363 A A 30 0 25 1 , I +chrM 2364 T T 30 0 25 1 , I +chrM 2365 T T 30 0 25 1 , I +chrM 2366 G G 30 0 25 1 , I +chrM 2367 A A 30 0 25 1 , I +chrM 2368 T T 30 0 25 1 , I +chrM 2369 C C 30 0 25 1 ,$ E +chrM 2389 G G 30 0 25 1 ^:, A +chrM 2390 G G 30 0 25 1 , 8 +chrM 2391 G G 30 0 25 1 , E +chrM 2392 A A 30 0 25 1 , I +chrM 2393 T T 30 0 25 1 , I +chrM 2394 A A 30 0 25 1 , I +chrM 2395 A A 30 0 25 1 , I +chrM 2396 C C 30 0 25 1 , 8 +chrM 2397 A A 30 0 25 1 , I +chrM 2398 G G 30 0 25 1 , I +chrM 2399 C C 30 0 25 1 , I +chrM 2400 G G 30 0 25 1 , I +chrM 2401 C C 30 0 25 1 , I +chrM 2402 A A 30 0 25 1 , I +chrM 2403 A A 30 0 25 1 , I +chrM 2404 T T 30 0 25 1 , I +chrM 2405 C C 30 0 25 1 , I +chrM 2406 C C 30 0 25 1 , I +chrM 2407 T T 30 0 25 1 , G +chrM 2408 A A 30 0 25 1 , I +chrM 2409 T T 30 0 25 1 , I +chrM 2410 T T 30 0 25 1 , B +chrM 2411 C C 30 0 25 1 , I +chrM 2412 C C 30 0 25 1 , I +chrM 2413 A A 30 0 25 1 , I +chrM 2414 G G 30 0 25 1 , I +chrM 2415 A A 30 0 25 1 , I +chrM 2416 G N 0 0 0 1 n " +chrM 2417 T N 0 0 0 1 n " +chrM 2418 C C 30 0 25 1 , I +chrM 2419 C C 30 0 25 1 , I +chrM 2420 A A 30 0 25 1 , I +chrM 2421 T T 30 0 25 1 , I +chrM 2422 A A 30 0 25 1 , I +chrM 2423 T T 30 0 25 1 , I +chrM 2424 C C 30 0 25 1 ,$ E +chrM 2735 t T 30 0 25 1 ^:, A +chrM 2736 t T 30 0 25 1 , 9 +chrM 2737 t T 30 0 25 1 , E +chrM 2738 a A 30 0 25 1 , I +chrM 2739 c C 30 0 25 1 , I +chrM 2740 a A 30 0 25 1 , I +chrM 2741 c C 30 0 25 1 , I +chrM 2742 t T 30 0 25 1 , 5 +chrM 2743 c C 30 0 25 1 , I +chrM 2744 a A 30 0 25 1 , I +chrM 2745 g G 30 0 25 1 , I +chrM 2746 a A 30 0 25 1 , I +chrM 2747 g G 30 0 25 1 , I +chrM 2748 g G 30 0 25 1 , I +chrM 2749 t T 30 0 25 1 , I +chrM 2750 t T 30 0 25 1 , I +chrM 2751 c C 30 0 25 1 , I +chrM 2752 a A 30 0 25 1 , I +chrM 2753 a A 30 0 25 1 , I +chrM 2754 c C 30 0 25 1 , I +chrM 2755 t T 30 0 25 1 , I +chrM 2756 c C 30 0 25 1 , I +chrM 2757 c C 30 0 25 1 , I +chrM 2758 t T 30 0 25 1 , I +chrM 2759 c C 30 0 25 1 , I +chrM 2760 t T 30 0 25 1 , I +chrM 2761 c C 30 0 25 1 , I +chrM 2762 c N 0 0 0 1 n " +chrM 2763 c N 0 0 0 1 n " +chrM 2764 t T 30 0 25 1 , I +chrM 2765 a A 30 0 25 1 , I +chrM 2766 a A 30 0 25 1 , I +chrM 2767 c C 30 0 25 1 , I +chrM 2768 a A 30 0 25 1 , I +chrM 2769 a A 30 0 25 1 , I +chrM 2770 c C 30 0 25 1 ,$ E +chrM 2844 G G 30 0 25 1 ^:. E +chrM 2845 A A 30 0 25 1 . I +chrM 2846 A A 30 0 25 1 . I +chrM 2847 A A 30 0 25 1 . I +chrM 2848 A A 30 0 25 1 . I +chrM 2849 G G 30 0 25 1 . I +chrM 2850 T T 30 0 25 1 . I +chrM 2851 C N 0 0 0 1 N " +chrM 2852 T N 0 0 0 1 N " +chrM 2853 T T 30 0 25 1 . I +chrM 2854 A A 30 0 25 1 . I +chrM 2855 G G 30 0 25 1 . I +chrM 2856 G G 30 0 25 1 . I +chrM 2857 C C 30 0 25 1 . I +chrM 2858 T T 30 0 25 1 . I +chrM 2859 A A 30 0 25 1 . I +chrM 2860 T T 30 0 25 1 . I +chrM 2861 A A 30 0 25 1 . B +chrM 2862 T T 30 0 25 1 . I +chrM 2863 G G 30 0 25 1 . I +chrM 2864 C C 30 0 25 1 . I +chrM 2865 A A 30 0 25 1 . I +chrM 2866 A A 30 0 25 1 . B +chrM 2867 C C 30 0 25 1 . I +chrM 2868 T T 30 0 25 1 . I +chrM 2869 T T 30 0 25 1 . I +chrM 2870 C C 30 0 25 1 . I +chrM 2871 G G 30 0 25 1 . = +chrM 2872 C C 30 0 25 1 . I +chrM 2873 A A 30 0 25 1 . @ +chrM 2874 A A 30 0 25 1 . 9 +chrM 2875 A A 30 0 25 1 . 6 +chrM 2876 G G 30 0 25 1 . D +chrM 2877 G G 30 0 25 1 . 2 +chrM 2878 A N 0 0 0 1 . * +chrM 2879 C C 30 0 25 1 .$ > +chrM 3080 T T 30 0 25 1 ^:. B +chrM 3081 T T 30 0 25 1 . E +chrM 3082 C C 30 0 25 1 . I +chrM 3083 A A 30 0 25 1 . I +chrM 3084 T T 30 0 25 1 . I +chrM 3085 A A 30 0 25 1 . I +chrM 3086 C C 30 0 25 1 . I +chrM 3087 T N 0 0 0 1 N " +chrM 3088 A N 0 0 0 1 N " +chrM 3089 G G 30 0 25 1 . I +chrM 3090 C C 30 0 25 1 . I +chrM 3091 C C 30 0 25 1 . I +chrM 3092 A A 30 0 25 1 . I +chrM 3093 T T 30 0 25 1 . I +chrM 3094 G G 30 0 25 1 . I +chrM 3095 T T 30 0 25 1 . I +chrM 3096 C C 30 0 25 1 . I +chrM 3097 C C 30 0 25 1 . I +chrM 3098 A A 30 0 25 1 . I +chrM 3099 G G 30 0 25 1 . H +chrM 3100 C C 30 0 25 1 . I +chrM 3101 C C 30 0 25 1 . I +chrM 3102 T T 30 0 25 1 . I +chrM 3103 A A 30 0 25 1 . I +chrM 3104 G G 30 0 25 1 . I +chrM 3105 C C 30 0 25 1 . I +chrM 3106 T T 30 0 25 1 . I +chrM 3107 G G 30 0 25 1 . I +chrM 3108 T T 30 0 25 1 . I +chrM 3109 C C 30 0 25 1 . I +chrM 3110 T T 30 0 25 1 . I +chrM 3111 A A 30 0 25 1 . < +chrM 3112 C C 30 0 25 1 . I +chrM 3113 T T 30 0 25 1 . I +chrM 3114 C C 30 0 25 1 . I +chrM 3115 A A 30 0 25 1 .$ > +chrM 3188 A A 30 0 25 1 ^:, E +chrM 3189 T T 30 0 25 1 , = +chrM 3190 C C 30 0 25 1 , I +chrM 3191 T T 30 0 25 1 , I +chrM 3192 C C 30 0 25 1 , I +chrM 3193 A A 30 0 25 1 , I +chrM 3194 T T 30 0 25 1 , I +chrM 3195 A A 30 0 25 1 , I +chrM 3196 C C 30 0 25 1 , I +chrM 3197 G G 30 0 25 1 , @ +chrM 3198 A A 30 0 25 1 , I +chrM 3199 A A 30 0 25 1 , I +chrM 3200 G G 30 0 25 1 , I +chrM 3201 T T 30 0 25 1 , I +chrM 3202 A A 30 0 25 1 , I +chrM 3203 A A 30 0 25 1 , I +chrM 3204 C C 30 0 25 1 , I +chrM 3205 T T 30 0 25 1 , I +chrM 3206 C C 30 0 25 1 , I +chrM 3207 T T 30 0 25 1 , I +chrM 3208 A A 30 0 25 1 , I +chrM 3209 G G 30 0 25 1 , I +chrM 3210 C C 30 0 25 1 , I +chrM 3211 A A 30 0 25 1 , I +chrM 3212 A A 30 0 25 1 , I +chrM 3213 T T 30 0 25 1 , I +chrM 3214 C C 30 0 25 1 , I +chrM 3215 A N 0 0 0 1 n " +chrM 3216 T N 0 0 0 1 n " +chrM 3217 C C 30 0 25 1 , I +chrM 3218 C C 30 0 25 1 , I +chrM 3219 T T 30 0 25 1 , I +chrM 3220 A A 30 0 25 1 , I +chrM 3221 C C 30 0 25 1 , I +chrM 3222 T T 30 0 25 1 , F +chrM 3223 C C 30 0 25 1 ,$ B +chrM 3502 A A 30 0 25 1 ^:. E +chrM 3503 G G 30 0 25 1 . I +chrM 3504 C C 30 0 25 1 . I +chrM 3505 A A 30 0 25 1 . I +chrM 3506 T T 30 0 25 1 . I +chrM 3507 T T 30 0 25 1 . I +chrM 3508 T T 30 0 25 1 . I +chrM 3509 C N 0 0 0 1 N " +chrM 3510 A N 0 0 0 1 N " +chrM 3511 C C 30 0 25 1 . I +chrM 3512 A A 30 0 25 1 . I +chrM 3513 A A 30 0 25 1 . I +chrM 3514 C C 30 0 25 1 . I +chrM 3515 C C 30 0 25 1 . I +chrM 3516 C C 30 0 25 1 . I +chrM 3517 C C 30 0 25 1 . I +chrM 3518 T T 30 0 25 1 . I +chrM 3519 A A 30 0 25 1 . I +chrM 3520 C C 30 0 25 1 . I +chrM 3521 C C 30 0 25 1 . I +chrM 3522 T T 30 0 25 1 . I +chrM 3523 G G 30 0 25 1 . I +chrM 3524 C C 30 0 25 1 . I +chrM 3525 C C 30 0 25 1 . I +chrM 3526 A A 30 0 25 1 . > +chrM 3527 G G 30 0 25 1 . I +chrM 3528 A A 30 0 25 1 . 4 +chrM 3529 A A 30 0 25 1 . @ +chrM 3530 C C 30 0 25 1 . I +chrM 3531 T T 30 0 25 1 . I +chrM 3532 C C 30 0 25 1 . I +chrM 3533 T T 30 0 25 1 . I +chrM 3534 A A 30 0 25 1 . I +chrM 3535 C C 30 0 25 1 . I +chrM 3536 T T 30 0 25 1 . I +chrM 3537 C C 30 0 25 1 .$ E +chrM 3678 G G 30 0 25 1 ^:. E +chrM 3679 A A 30 0 25 1 . I +chrM 3680 C C 30 0 25 1 . I +chrM 3681 A A 30 0 25 1 . I +chrM 3682 C C 30 0 25 1 . I +chrM 3683 G G 30 0 25 1 . I +chrM 3684 T T 30 0 25 1 . I +chrM 3685 C N 0 0 0 1 N " +chrM 3686 T N 0 0 0 1 N " +chrM 3687 C C 30 0 25 1 . I +chrM 3688 A A 30 0 25 1 . I +chrM 3689 C C 30 0 25 1 . I +chrM 3690 T T 30 0 25 1 . I +chrM 3691 T T 30 0 25 1 . I +chrM 3692 C C 30 0 25 1 . I +chrM 3693 C C 30 0 25 1 . I +chrM 3694 A A 30 0 25 1 . I +chrM 3695 A A 30 0 25 1 . : +chrM 3696 T T 30 0 25 1 . I +chrM 3697 C C 30 0 25 1 . I +chrM 3698 A A 30 0 25 1 . I +chrM 3699 T T 30 0 25 1 . I +chrM 3700 A A 30 0 25 1 . 8 +chrM 3701 C C 30 0 25 1 . I +chrM 3702 T T 30 0 25 1 . I +chrM 3703 A A 30 0 25 1 . E +chrM 3704 T T 30 0 25 1 . I +chrM 3705 C C 30 0 25 1 . I +chrM 3706 C C 30 0 25 1 . I +chrM 3707 A A 30 0 25 1 . I +chrM 3708 G N 0 0 0 1 . - +chrM 3709 C C 30 0 25 1 . I +chrM 3710 A A 30 0 25 1 . A +chrM 3711 T T 30 0 25 1 . I +chrM 3712 C C 30 0 25 1 . > +chrM 3713 C C 30 0 25 1 .$ ; +chrM 3753 T T 30 0 25 1 ^:. A +chrM 3754 T T 30 0 25 1 . B +chrM 3755 T T 30 0 25 1 . E +chrM 3756 G G 30 0 25 1 . I +chrM 3757 A A 30 0 25 1 . I +chrM 3758 T T 30 0 25 1 . I +chrM 3759 A A 30 0 25 1 . I +chrM 3760 G N 0 0 0 1 N " +chrM 3761 A N 0 0 0 1 N " +chrM 3762 G G 30 0 25 1 . I +chrM 3763 T T 30 0 25 1 . I +chrM 3764 A A 30 0 25 1 . I +chrM 3765 A A 30 0 25 1 . I +chrM 3766 A A 30 0 25 1 . I +chrM 3767 A A 30 0 25 1 . I +chrM 3768 C C 30 0 25 1 . I +chrM 3769 A A 30 0 25 1 . I +chrM 3770 T T 30 0 25 1 . I +chrM 3771 A A 30 0 25 1 . I +chrM 3772 G G 30 0 25 1 . I +chrM 3773 A A 30 0 25 1 . I +chrM 3774 G G 30 0 25 1 . I +chrM 3775 G G 30 0 25 1 . I +chrM 3776 C C 30 0 25 1 . I +chrM 3777 T T 30 0 25 1 . I +chrM 3778 C C 30 0 25 1 . I +chrM 3779 A A 30 0 25 1 . C +chrM 3780 A A 30 0 25 1 . I +chrM 3781 A A 30 0 25 1 . I +chrM 3782 C C 30 0 25 1 . I +chrM 3783 C C 30 0 25 1 . I +chrM 3784 C C 30 0 25 1 . I +chrM 3785 T T 30 0 25 1 . I +chrM 3786 C C 30 0 25 1 . I +chrM 3787 T T 30 0 25 1 . E +chrM 3788 T T 30 0 25 1 .$ A +chrM 3841 t T 30 0 25 1 ^:, E +chrM 3842 g G 30 0 25 1 , I +chrM 3843 c N 0 0 0 1 , + +chrM 3844 t T 30 0 25 1 , I +chrM 3845 a A 30 0 25 1 , I +chrM 3846 c N 0 0 0 1 , % +chrM 3847 c N 0 0 0 1 , ( +chrM 3848 g G 30 0 25 1 , I +chrM 3849 a A 30 0 25 1 , I +chrM 3850 a A 30 0 25 1 , I +chrM 3851 t T 30 0 25 1 , I +chrM 3852 t T 30 0 25 1 , I +chrM 3853 a A 30 0 25 1 , I +chrM 3854 c C 30 0 25 1 , I +chrM 3855 a A 30 0 25 1 , I +chrM 3856 c C 30 0 25 1 , I +chrM 3857 c C 30 0 25 1 , I +chrM 3858 a A 30 0 25 1 , I +chrM 3859 t T 30 0 25 1 , I +chrM 3860 g G 30 0 25 1 , I +chrM 3861 t T 30 0 25 1 , I +chrM 3862 c C 30 0 25 1 , I +chrM 3863 c C 30 0 25 1 , I +chrM 3864 t T 30 0 25 1 , I +chrM 3865 a A 30 0 25 1 , I +chrM 3866 C C 30 0 25 1 , I +chrM 3867 A A 30 0 25 1 , I +chrM 3868 A N 0 0 0 1 n " +chrM 3869 G N 0 0 0 1 n " +chrM 3870 T T 30 0 25 1 , I +chrM 3871 A A 30 0 25 1 , I +chrM 3872 A A 30 0 25 1 , I +chrM 3873 G G 30 0 25 1 , I +chrM 3874 G G 30 0 25 1 , I +chrM 3875 T T 30 0 25 1 , I +chrM 3876 C C 30 0 25 1 ,$ E +chrM 3921 C C 30 0 25 1 ^:, E +chrM 3922 A A 30 0 25 1 , I +chrM 3923 C C 30 0 25 1 , I +chrM 3924 C C 30 0 25 1 , I +chrM 3925 C C 30 0 25 1 , I +chrM 3926 T T 30 0 25 1 , = +chrM 3927 T T 30 0 25 1 , A +chrM 3928 C C 30 0 25 1 , I +chrM 3929 C C 30 0 25 1 , I +chrM 3930 C C 30 0 25 1 , I +chrM 3931 G G 30 0 25 1 , I +chrM 3932 T T 30 0 25 1 , I +chrM 3933 A A 30 0 25 1 , I +chrM 3934 C C 30 0 25 1 , I +chrM 3935 T T 30 0 25 1 , I +chrM 3936 A A 30 0 25 1 , I +chrM 3937 A A 30 0 25 1 , I +chrM 3938 T T 30 0 25 1 , I +chrM 3939 A A 30 0 25 1 , I +chrM 3940 A A 30 0 25 1 , I +chrM 3941 A A 30 0 25 1 , I +chrM 3942 T T 30 0 25 1 , B +chrM 3943 C C 30 0 25 1 , I +chrM 3944 C C 30 0 25 1 , I +chrM 3945 C C 30 0 25 1 , I +chrM 3946 C C 30 0 25 1 , I +chrM 3947 T T 30 0 25 1 , I +chrM 3948 T N 0 0 0 1 n " +chrM 3949 A N 0 0 0 1 n " +chrM 3950 T T 30 0 25 1 , I +chrM 3951 C C 30 0 25 1 , I +chrM 3952 T T 30 0 25 1 , I +chrM 3953 T T 30 0 25 1 , I +chrM 3954 C C 30 0 25 1 , I +chrM 3955 A A 30 0 25 1 , I +chrM 3956 C C 30 0 25 1 ,$ E +chrM 4249 A A 30 0 25 1 ^:, ; +chrM 4250 A A 30 0 25 1 , ; +chrM 4251 A A 30 0 25 1 , > +chrM 4252 C C 30 0 25 1 , I +chrM 4253 T T 30 0 25 1 , 5 +chrM 4254 T T 30 0 25 1 , 6 +chrM 4255 G G 30 0 25 1 , I +chrM 4256 G G 30 0 25 1 , I +chrM 4257 A A 30 0 25 1 , I +chrM 4258 C C 30 0 25 1 , I +chrM 4259 T T 30 0 25 1 , I +chrM 4260 C C 30 0 25 1 , I +chrM 4261 A A 30 0 25 1 , I +chrM 4262 C C 30 0 25 1 , I +chrM 4263 A A 30 0 25 1 , I +chrM 4264 C C 30 0 25 1 , I +chrM 4265 C C 30 0 25 1 , I +chrM 4266 A A 30 0 25 1 , I +chrM 4267 T T 30 0 25 1 , I +chrM 4268 T T 30 0 25 1 , I +chrM 4269 C C 30 0 25 1 , I +chrM 4270 C C 30 0 25 1 , I +chrM 4271 A A 30 0 25 1 , I +chrM 4272 C C 30 0 25 1 , I +chrM 4273 T T 30 0 25 1 , I +chrM 4274 T T 30 0 25 1 , I +chrM 4275 C C 30 0 25 1 , I +chrM 4276 T N 0 0 0 1 n " +chrM 4277 G N 0 0 0 1 n " +chrM 4278 A A 30 0 25 1 , I +chrM 4279 G G 30 0 25 1 , I +chrM 4280 T T 30 0 25 1 , I +chrM 4281 A A 30 0 25 1 , I +chrM 4282 C C 30 0 25 1 , E +chrM 4283 C C 30 0 25 1 , B +chrM 4284 C C 30 0 25 1 ,$ @ +chrM 4552 T T 30 0 25 1 ^:. B +chrM 4553 T T 30 0 25 1 . E +chrM 4554 A A 30 0 25 1 . I +chrM 4555 A A 30 0 25 1 . I +chrM 4556 T T 30 0 25 1 . I +chrM 4557 T T 30 0 25 1 . I +chrM 4558 T T 30 0 25 1 . I +chrM 4559 A N 0 0 0 1 N " +chrM 4560 C N 0 0 0 1 N " +chrM 4561 A A 30 0 25 1 . I +chrM 4562 T T 30 0 25 1 . I +chrM 4563 T T 30 0 25 1 . I +chrM 4564 A A 30 0 25 1 . I +chrM 4565 T T 30 0 25 1 . I +chrM 4566 A A 30 0 25 1 . I +chrM 4567 A A 30 0 25 1 . I +chrM 4568 T T 30 0 25 1 . I +chrM 4569 A A 30 0 25 1 . I +chrM 4570 A A 30 0 25 1 . I +chrM 4571 C C 30 0 25 1 . I +chrM 4572 A A 30 0 25 1 . I +chrM 4573 C C 30 0 25 1 . I +chrM 4574 T T 30 0 25 1 . I +chrM 4575 C C 30 0 25 1 . I +chrM 4576 A A 30 0 25 1 . I +chrM 4577 C C 30 0 25 1 . I +chrM 4578 A A 30 0 25 1 . I +chrM 4579 A A 30 0 25 1 . ? +chrM 4580 T T 30 0 25 1 . I +chrM 4581 A A 30 0 25 1 . 6 +chrM 4582 T T 30 0 25 1 . I +chrM 4583 T T 30 0 25 1 . I +chrM 4584 C C 30 0 25 1 . I +chrM 4585 A A 30 0 25 1 . I +chrM 4586 T T 30 0 25 1 . I +chrM 4587 A A 30 0 25 1 .$ 6 +chrM 4697 T T 30 0 25 1 ^:, 5 +chrM 4698 C C 30 0 25 1 , = +chrM 4699 C C 30 0 25 1 , 4 +chrM 4700 C N 0 0 0 1 , & +chrM 4701 C C 30 0 25 1 , G +chrM 4702 C C 30 0 25 1 , 1 +chrM 4703 C C 30 0 25 1 , 3 +chrM 4704 A A 30 0 25 1 , I +chrM 4705 C C 30 0 25 1 , . +chrM 4706 T T 30 0 25 1 , ? +chrM 4707 A A 30 0 25 1 , I +chrM 4708 T T 30 0 25 1 , I +chrM 4709 C C 30 0 25 1 , I +chrM 4710 A A 30 0 25 1 , I +chrM 4711 G G 30 0 25 1 , I +chrM 4712 G G 30 0 25 1 , I +chrM 4713 A A 30 0 25 1 , I +chrM 4714 T T 30 0 25 1 , I +chrM 4715 T T 30 0 25 1 , I +chrM 4716 C C 30 0 25 1 , I +chrM 4717 A A 30 0 25 1 , I +chrM 4718 T T 30 0 25 1 , I +chrM 4719 A A 30 0 25 1 , I +chrM 4720 C C 30 0 25 1 , I +chrM 4721 C C 30 0 25 1 , I +chrM 4722 C C 30 0 25 1 , I +chrM 4723 A A 30 0 25 1 , I +chrM 4724 A N 0 0 0 1 n " +chrM 4725 A N 0 0 0 1 n " +chrM 4726 T T 30 0 25 1 , I +chrM 4727 G G 30 0 25 1 , I +chrM 4728 A A 30 0 25 1 , I +chrM 4729 A A 30 0 25 1 , I +chrM 4730 T T 30 0 25 1 , I +chrM 4731 A A 30 0 25 1 , E +chrM 4732 A A 30 0 25 1 ,$ B +chrM 4742 A A 30 0 25 1 ^:. D +chrM 4743 G G 30 0 25 1 . I +chrM 4744 C C 30 0 25 1 . I +chrM 4745 T T 30 0 25 1 . I +chrM 4746 C C 30 0 25 1 . I +chrM 4747 A A 30 0 25 1 . I +chrM 4748 C C 30 0 25 1 . I +chrM 4749 C N 0 0 0 1 N " +chrM 4750 A N 0 0 0 1 N " +chrM 4751 A A 30 0 25 1 . I +chrM 4752 A A 30 0 25 1 . I +chrM 4753 A A 30 0 25 1 . I +chrM 4754 A A 30 0 25 1 . I +chrM 4755 T T 30 0 25 1 . I +chrM 4756 A A 30 0 25 1 . I +chrM 4757 G G 30 0 25 1 . I +chrM 4758 C C 30 0 25 1 . I +chrM 4759 A A 30 0 25 1 . I +chrM 4760 G G 30 0 25 1 . I +chrM 4761 C C 30 0 25 1 . I +chrM 4762 A A 30 0 25 1 . I +chrM 4763 T T 30 0 25 1 . I +chrM 4764 C C 30 0 25 1 . I +chrM 4765 A A 30 0 25 1 . I +chrM 4766 T T 30 0 25 1 . I +chrM 4767 C C 30 0 25 1 . I +chrM 4768 C C 30 0 25 1 . I +chrM 4769 T T 30 0 25 1 . I +chrM 4770 C C 30 0 25 1 . I +chrM 4771 C C 30 0 25 1 . I +chrM 4772 C C 30 0 25 1 . I +chrM 4773 C C 30 0 25 1 . I +chrM 4774 A A 30 0 25 1 . 8 +chrM 4775 C C 30 0 25 1 . I +chrM 4776 A A 30 0 25 1 . : +chrM 4777 C C 30 0 25 1 .$ E +chrM 4932 C C 30 0 25 1 ^:, E +chrM 4933 T N 0 0 0 1 , - +chrM 4934 C C 30 0 25 1 , A +chrM 4935 C C 30 0 25 1 , I +chrM 4936 C C 30 0 25 1 , I +chrM 4937 T T 30 0 25 1 , 7 +chrM 4938 A A 30 0 25 1 , I +chrM 4939 C C 30 0 25 1 , I +chrM 4940 T T 30 0 25 1 , 5 +chrM 4941 C C 30 0 25 1 , I +chrM 4942 C C 30 0 25 1 , I +chrM 4943 T T 30 0 25 1 , : +chrM 4944 C C 30 0 25 1 , I +chrM 4945 C C 30 0 25 1 , I +chrM 4946 C C 30 0 25 1 , I +chrM 4947 C C 30 0 25 1 , I +chrM 4948 C C 30 0 25 1 , I +chrM 4949 T T 30 0 25 1 , I +chrM 4950 A A 30 0 25 1 , I +chrM 4951 A A 30 0 25 1 , I +chrM 4952 C C 30 0 25 1 , I +chrM 4953 C C 30 0 25 1 , I +chrM 4954 C C 30 0 25 1 , I +chrM 4955 C C 30 0 25 1 , I +chrM 4956 C C 30 0 25 1 , I +chrM 4957 A A 30 0 25 1 , I +chrM 4958 T T 30 0 25 1 , I +chrM 4959 A N 0 0 0 1 n " +chrM 4960 C N 0 0 0 1 n " +chrM 4961 T T 30 0 25 1 , I +chrM 4962 A A 30 0 25 1 , I +chrM 4963 T T 30 0 25 1 , I +chrM 4964 C C 30 0 25 1 , I +chrM 4965 A A 30 0 25 1 , I +chrM 4966 A A 30 0 25 1 , I +chrM 4967 T T 30 0 25 1 ,$ > +chrM 5155 G G 30 0 25 1 ^:, 7 +chrM 5156 T T 30 0 25 1 , I +chrM 5157 T T 30 0 25 1 , I +chrM 5158 A A 30 0 25 1 , I +chrM 5159 A A 30 0 25 1 , I +chrM 5160 C C 30 0 25 1 , I +chrM 5161 A A 30 0 25 1 , I +chrM 5162 G G 30 0 25 1 , I +chrM 5163 C C 30 0 25 1 , I +chrM 5164 T T 30 0 25 1 , I +chrM 5165 A A 30 0 25 1 , I +chrM 5166 A A 30 0 25 1 , I +chrM 5167 A A 30 0 25 1 , I +chrM 5168 T T 30 0 25 1 , I +chrM 5169 A A 30 0 25 1 , I +chrM 5170 C C 30 0 25 1 , I +chrM 5171 C C 30 0 25 1 , I +chrM 5172 C C 30 0 25 1 , I +chrM 5173 T T 30 0 25 1 , I +chrM 5174 A A 30 0 25 1 , I +chrM 5175 A A 30 0 25 1 , I +chrM 5176 T T 30 0 25 1 , I +chrM 5177 C C 30 0 25 1 , I +chrM 5178 A A 30 0 25 1 , I +chrM 5179 A A 30 0 25 1 , I +chrM 5180 C C 30 0 25 1 , I +chrM 5181 T T 30 0 25 1 , I +chrM 5182 G N 0 0 0 1 n " +chrM 5183 G N 0 0 0 1 n " +chrM 5184 C C 30 0 25 1 , I +chrM 5185 T T 30 0 25 1 , I +chrM 5186 T T 30 0 25 1 , I +chrM 5187 C C 30 0 25 1 , I +chrM 5188 A A 30 0 25 1 , I +chrM 5189 A A 30 0 25 1 , I +chrM 5190 T T 30 0 25 1 ,$ D +chrM 5309 T T 30 0 25 1 ^:, E +chrM 5310 C C 30 0 25 1 , I +chrM 5311 C C 30 0 25 1 , I +chrM 5312 A A 30 0 25 1 , I +chrM 5313 A A 30 0 25 1 , I +chrM 5314 C C 30 0 25 1 , I +chrM 5315 C C 30 0 25 1 , I +chrM 5316 C C 30 0 25 1 , I +chrM 5317 C C 30 0 25 1 , I +chrM 5318 T T 30 0 25 1 , I +chrM 5319 G G 30 0 25 1 , I +chrM 5320 T T 30 0 25 1 , I +chrM 5321 C C 30 0 25 1 , I +chrM 5322 T T 30 0 25 1 , I +chrM 5323 T T 30 0 25 1 , I +chrM 5324 T T 30 0 25 1 , I +chrM 5325 A A 30 0 25 1 , I +chrM 5326 G G 30 0 25 1 , I +chrM 5327 A A 30 0 25 1 , I +chrM 5328 T T 30 0 25 1 , I +chrM 5329 T T 30 0 25 1 , I +chrM 5330 T T 30 0 25 1 , I +chrM 5331 A A 30 0 25 1 , I +chrM 5332 C C 30 0 25 1 , I +chrM 5333 A A 30 0 25 1 , I +chrM 5334 G G 30 0 25 1 , I +chrM 5335 T T 30 0 25 1 , I +chrM 5336 C N 0 0 0 1 n " +chrM 5337 T N 0 0 0 1 n " +chrM 5338 A A 30 0 25 1 , I +chrM 5339 A A 30 0 25 1 , I +chrM 5340 T T 30 0 25 1 , I +chrM 5341 G G 30 0 25 1 , I +chrM 5342 C C 30 0 25 1 , I +chrM 5343 T T 30 0 25 1 , E +chrM 5344 T T 30 0 25 1 ,$ B +chrM 5540 C C 30 0 25 1 ^:, ? +chrM 5541 C C 30 0 25 1 , : +chrM 5542 C C 30 0 25 1 , ; +chrM 5543 A A 30 0 25 1 , I +chrM 5544 T T 30 0 25 1 , 9 +chrM 5545 G G 30 0 25 1 , D +chrM 5546 C C 30 0 25 1 , D +chrM 5547 A A 30 0 25 1 , I +chrM 5548 T T 30 0 25 1 , B +chrM 5549 T T 30 0 25 1 , E +chrM 5550 C C 30 0 25 1 , I +chrM 5551 G G 30 0 25 1 , I +chrM 5552 T T 30 0 25 1 , I +chrM 5553 A A 30 0 25 1 , I +chrM 5554 A A 30 0 25 1 , I +chrM 5555 T T 30 0 25 1 , I +chrM 5556 A A 30 0 25 1 , I +chrM 5557 A A 30 0 25 1 , I +chrM 5558 T T 30 0 25 1 , E +chrM 5559 T T 30 0 25 1 , I +chrM 5560 T T 30 0 25 1 , E +chrM 5561 T T 30 0 25 1 , I +chrM 5562 C C 30 0 25 1 , I +chrM 5563 T T 30 0 25 1 , I +chrM 5564 T T 30 0 25 1 , I +chrM 5565 T T 30 0 25 1 , I +chrM 5566 A A 30 0 25 1 , I +chrM 5567 T N 0 0 0 1 n " +chrM 5568 G N 0 0 0 1 n " +chrM 5569 G G 30 0 25 1 , I +chrM 5570 T T 30 0 25 1 , I +chrM 5571 C C 30 0 25 1 , I +chrM 5572 A A 30 0 25 1 , I +chrM 5573 T T 30 0 25 1 , I +chrM 5574 A A 30 0 25 1 , I +chrM 5575 C C 30 0 25 1 ,$ > +chrM 6016 T T 30 0 25 1 ^:, > +chrM 6017 T T 30 0 25 1 , 7 +chrM 6018 C C 30 0 25 1 , I +chrM 6019 T T 30 0 25 1 , < +chrM 6020 T T 30 0 25 1 , ? +chrM 6021 C C 30 0 25 1 , I +chrM 6022 G G 30 0 25 1 , I +chrM 6023 A A 30 0 25 1 , I +chrM 6024 C C 30 0 25 1 , I +chrM 6025 C C 30 0 25 1 , I +chrM 6026 C C 30 0 25 1 , I +chrM 6027 C C 30 0 25 1 , I +chrM 6028 G G 30 0 25 1 , I +chrM 6029 C C 30 0 25 1 , I +chrM 6030 A A 30 0 25 1 , I +chrM 6031 G G 30 0 25 1 , I +chrM 6032 G G 30 0 25 1 , I +chrM 6033 A A 30 0 25 1 , I +chrM 6034 G G 30 0 25 1 , I +chrM 6035 G G 30 0 25 1 , I +chrM 6036 A A 30 0 25 1 , I +chrM 6037 G G 30 0 25 1 , I +chrM 6038 G G 30 0 25 1 , I +chrM 6039 G G 30 0 25 1 , I +chrM 6040 G G 33 0 25 2 ,^:. IE chrM 6041 A A 33 0 25 2 ,. II chrM 6042 T T 33 0 25 2 ,. II -chrM 6043 C C 19 0 25 2 n. "I -chrM 6044 C C 19 0 25 2 n. "I +chrM 6043 C C 30 0 25 2 n. "I +chrM 6044 C C 30 0 25 2 n. "I chrM 6045 A A 33 0 25 2 ,. II chrM 6046 A A 33 0 25 2 ,. II -chrM 6047 T T 19 0 25 2 ,N I" -chrM 6048 C C 19 0 25 2 ,N I" +chrM 6047 T T 30 0 25 2 ,N I" +chrM 6048 C C 30 0 25 2 ,N I" chrM 6049 C C 33 0 25 2 ,. II -chrM 6050 T T 33 0 25 2 ,. II -chrM 6051 T T 33 0 25 2 ,$. II -chrM 6052 T T 25 0 25 1 . I -chrM 6053 A A 33 0 25 2 .^:. II +chrM 6050 T T 33 0 25 2 ,. >I +chrM 6051 T T 33 0 25 2 ,$. ;I +chrM 6052 T T 30 0 25 1 . I +chrM 6053 A A 33 0 25 2 .^:. IE chrM 6054 T T 33 0 25 2 .. II chrM 6055 C C 33 0 25 2 .. II chrM 6056 A A 33 0 25 2 .. II chrM 6057 A A 33 0 25 2 .. II chrM 6058 C C 33 0 25 2 .. II chrM 6059 A A 33 0 25 2 .. II -chrM 6060 C C 19 0 25 2 .N I" -chrM 6061 C C 19 0 25 2 .N I" +chrM 6060 C C 30 0 25 2 .N I" +chrM 6061 C C 30 0 25 2 .N I" chrM 6062 T T 33 0 25 2 .. II chrM 6063 A A 33 0 25 2 .. II chrM 6064 T T 33 0 25 2 .. II @@ -1066,109 +1066,109 @@ chrM 6071 T T 33 0 25 2 .. II chrM 6072 C C 33 0 25 2 .. II chrM 6073 T T 33 0 25 2 .. II chrM 6074 T T 33 0 25 2 .. II -chrM 6075 C C 33 0 25 2 .$. II -chrM 6076 G G 25 0 25 1 . I -chrM 6077 G G 25 0 25 1 . I -chrM 6078 A A 25 0 25 1 . I -chrM 6079 C C 25 0 25 1 . I -chrM 6080 A A 25 0 25 1 . A -chrM 6081 C C 25 0 25 1 . I -chrM 6082 C C 25 0 25 1 . I -chrM 6083 C C 25 0 25 1 . I -chrM 6084 C C 25 0 25 1 . I -chrM 6085 G G 25 0 25 1 . F -chrM 6086 A A 7 0 25 1 . ( -chrM 6087 A A 13 0 25 1 . . -chrM 6088 G G 25 0 25 1 .$ I -chrM 6379 T T 25 0 25 1 ^:. I -chrM 6380 G G 25 0 25 1 . I -chrM 6381 A A 25 0 25 1 . I -chrM 6382 G G 25 0 25 1 . I -chrM 6383 C C 25 0 25 1 . I -chrM 6384 T T 25 0 25 1 . I -chrM 6385 C C 25 0 25 1 . I -chrM 6386 T A 4 4 25 1 N " -chrM 6387 A A 4 0 25 1 N " -chrM 6388 G G 25 0 25 1 . I -chrM 6389 G G 25 0 25 1 . I -chrM 6390 C C 25 0 25 1 . I -chrM 6391 T T 25 0 25 1 . I -chrM 6392 T T 25 0 25 1 . I -chrM 6393 C C 25 0 25 1 . I -chrM 6394 A A 25 0 25 1 . C -chrM 6395 T T 25 0 25 1 . I -chrM 6396 C C 25 0 25 1 . I -chrM 6397 T T 25 0 25 1 . I -chrM 6398 T T 25 0 25 1 . I -chrM 6399 C C 25 0 25 1 . I -chrM 6400 T T 25 0 25 1 . I -chrM 6401 T T 25 0 25 1 . I -chrM 6402 A A 25 0 25 1 . I -chrM 6403 T T 25 0 25 1 . I -chrM 6404 T T 25 0 25 1 . I -chrM 6405 C C 25 0 25 1 . I -chrM 6406 A A 25 0 25 1 . I -chrM 6407 C C 25 0 25 1 . I -chrM 6408 A A 25 0 25 1 . I -chrM 6409 G G 25 0 25 1 . @ -chrM 6410 T T 25 0 25 1 . I -chrM 6411 A A 25 0 25 1 . I -chrM 6412 G G 20 0 25 1 . 5 -chrM 6413 G G 25 0 25 1 . @ -chrM 6414 A A 25 0 25 1 .$ F -chrM 6591 A A 25 0 25 1 ^:. I -chrM 6592 A A 25 0 25 1 . I -chrM 6593 A A 25 0 25 1 . I -chrM 6594 A A 25 0 25 1 . I -chrM 6595 A A 25 0 25 1 . I -chrM 6596 T T 25 0 25 1 . I -chrM 6597 C C 25 0 25 1 . I -chrM 6598 C A 4 4 25 1 N " -chrM 6599 A A 4 0 25 1 N " -chrM 6600 C C 25 0 25 1 . I -chrM 6601 T T 25 0 25 1 . I -chrM 6602 T T 25 0 25 1 . I -chrM 6603 T T 25 0 25 1 . I -chrM 6604 A A 25 0 25 1 . I -chrM 6605 C C 25 0 25 1 . I -chrM 6606 A A 25 0 25 1 . I -chrM 6607 A A 25 0 25 1 . I -chrM 6608 T T 25 0 25 1 . I -chrM 6609 T T 25 0 25 1 . I -chrM 6610 A A 25 0 25 1 . I -chrM 6611 T T 25 0 25 1 . I -chrM 6612 A A 25 0 25 1 . I -chrM 6613 T T 25 0 25 1 . I -chrM 6614 T T 25 0 25 1 . I -chrM 6615 C C 25 0 25 1 . I -chrM 6616 G G 25 0 25 1 . F -chrM 6617 T T 25 0 25 1 . I -chrM 6618 A A 25 0 25 1 . I -chrM 6619 G G 25 0 25 1 . I -chrM 6620 G G 21 0 25 1 . 6 -chrM 6621 G G 25 0 25 1 . A -chrM 6622 G G 25 0 25 1 . I -chrM 6623 T T 25 0 25 1 . I -chrM 6624 A A 25 0 25 1 . I -chrM 6625 A A 25 0 25 1 . G -chrM 6626 A A 25 0 25 1 .$ I -chrM 6695 A A 25 0 25 1 ^:. I -chrM 6696 C C 25 0 25 1 . I -chrM 6697 G G 25 0 25 1 . I -chrM 6698 C C 25 0 25 1 . I -chrM 6699 A A 25 0 25 1 . I -chrM 6700 T T 25 0 25 1 . I -chrM 6701 A A 25 0 25 1 . I -chrM 6702 T A 4 4 25 1 N " -chrM 6703 A A 28 0 25 2 N^:. "I +chrM 6075 C C 33 0 25 2 .$. EI +chrM 6076 G G 30 0 25 1 . I +chrM 6077 G G 30 0 25 1 . I +chrM 6078 A A 30 0 25 1 . I +chrM 6079 C C 30 0 25 1 . I +chrM 6080 A A 30 0 25 1 . A +chrM 6081 C C 30 0 25 1 . I +chrM 6082 C C 30 0 25 1 . I +chrM 6083 C C 30 0 25 1 . I +chrM 6084 C C 30 0 25 1 . I +chrM 6085 G G 30 0 25 1 . F +chrM 6086 A N 0 0 0 1 . ( +chrM 6087 A A 30 0 25 1 . . +chrM 6088 G G 30 0 25 1 .$ E +chrM 6379 T T 30 0 25 1 ^:. E +chrM 6380 G G 30 0 25 1 . I +chrM 6381 A A 30 0 25 1 . I +chrM 6382 G G 30 0 25 1 . I +chrM 6383 C C 30 0 25 1 . I +chrM 6384 T T 30 0 25 1 . I +chrM 6385 C C 30 0 25 1 . I +chrM 6386 T N 0 0 0 1 N " +chrM 6387 A N 0 0 0 1 N " +chrM 6388 G G 30 0 25 1 . I +chrM 6389 G G 30 0 25 1 . I +chrM 6390 C C 30 0 25 1 . I +chrM 6391 T T 30 0 25 1 . I +chrM 6392 T T 30 0 25 1 . I +chrM 6393 C C 30 0 25 1 . I +chrM 6394 A A 30 0 25 1 . C +chrM 6395 T T 30 0 25 1 . I +chrM 6396 C C 30 0 25 1 . I +chrM 6397 T T 30 0 25 1 . I +chrM 6398 T T 30 0 25 1 . I +chrM 6399 C C 30 0 25 1 . I +chrM 6400 T T 30 0 25 1 . I +chrM 6401 T T 30 0 25 1 . I +chrM 6402 A A 30 0 25 1 . I +chrM 6403 T T 30 0 25 1 . I +chrM 6404 T T 30 0 25 1 . I +chrM 6405 C C 30 0 25 1 . I +chrM 6406 A A 30 0 25 1 . I +chrM 6407 C C 30 0 25 1 . I +chrM 6408 A A 30 0 25 1 . I +chrM 6409 G G 30 0 25 1 . @ +chrM 6410 T T 30 0 25 1 . I +chrM 6411 A A 30 0 25 1 . I +chrM 6412 G G 30 0 25 1 . 5 +chrM 6413 G G 30 0 25 1 . @ +chrM 6414 A A 30 0 25 1 .$ E +chrM 6591 A A 30 0 25 1 ^:. > +chrM 6592 A A 30 0 25 1 . ? +chrM 6593 A A 30 0 25 1 . A +chrM 6594 A A 30 0 25 1 . B +chrM 6595 A A 30 0 25 1 . E +chrM 6596 T T 30 0 25 1 . I +chrM 6597 C C 30 0 25 1 . I +chrM 6598 C N 0 0 0 1 N " +chrM 6599 A N 0 0 0 1 N " +chrM 6600 C C 30 0 25 1 . I +chrM 6601 T T 30 0 25 1 . I +chrM 6602 T T 30 0 25 1 . I +chrM 6603 T T 30 0 25 1 . I +chrM 6604 A A 30 0 25 1 . I +chrM 6605 C C 30 0 25 1 . I +chrM 6606 A A 30 0 25 1 . I +chrM 6607 A A 30 0 25 1 . I +chrM 6608 T T 30 0 25 1 . I +chrM 6609 T T 30 0 25 1 . I +chrM 6610 A A 30 0 25 1 . I +chrM 6611 T T 30 0 25 1 . I +chrM 6612 A A 30 0 25 1 . I +chrM 6613 T T 30 0 25 1 . I +chrM 6614 T T 30 0 25 1 . I +chrM 6615 C C 30 0 25 1 . I +chrM 6616 G G 30 0 25 1 . F +chrM 6617 T T 30 0 25 1 . I +chrM 6618 A A 30 0 25 1 . I +chrM 6619 G G 30 0 25 1 . I +chrM 6620 G G 30 0 25 1 . 6 +chrM 6621 G G 30 0 25 1 . A +chrM 6622 G G 30 0 25 1 . I +chrM 6623 T T 30 0 25 1 . I +chrM 6624 A A 30 0 25 1 . E +chrM 6625 A A 30 0 25 1 . B +chrM 6626 A A 30 0 25 1 .$ @ +chrM 6695 A A 30 0 25 1 ^:. E +chrM 6696 C C 30 0 25 1 . I +chrM 6697 G G 30 0 25 1 . I +chrM 6698 C C 30 0 25 1 . I +chrM 6699 A A 30 0 25 1 . I +chrM 6700 T T 30 0 25 1 . I +chrM 6701 A A 30 0 25 1 . I +chrM 6702 T N 0 0 0 1 N " +chrM 6703 A A 30 0 25 2 N^:. "E chrM 6704 C C 33 0 25 2 .. II chrM 6705 A A 33 0 25 2 .. II chrM 6706 A A 33 0 25 2 .. II chrM 6707 C C 33 0 25 2 .. II chrM 6708 A A 33 0 25 2 .. II chrM 6709 T T 33 0 25 2 .. II -chrM 6710 G G 19 0 25 2 .N I" -chrM 6711 A A 28 0 25 2 .N I" +chrM 6710 G G 30 0 25 2 .N I" +chrM 6711 A A 30 0 25 2 .N I" chrM 6712 A A 33 0 25 2 .. II chrM 6713 A A 33 0 25 2 .. II chrM 6714 T T 33 0 25 2 .. II @@ -1187,489 +1187,489 @@ chrM 6726 C C 33 0 25 2 .. II chrM 6727 A A 33 0 25 2 .. I> chrM 6728 T T 33 0 25 2 .. II chrM 6729 A A 33 0 25 2 .. GI -chrM 6730 G G 33 0 25 2 .$. IH -chrM 6731 G G 25 0 25 1 . I -chrM 6732 A A 25 0 25 1 . = -chrM 6733 T T 25 0 25 1 . I -chrM 6734 C C 25 0 25 1 . I -chrM 6735 T T 25 0 25 1 . I -chrM 6736 T T 25 0 25 1 . I -chrM 6737 T T 25 0 25 1 . I -chrM 6738 T T 25 0 25 1 .$ I -chrM 6809 C C 8 0 25 1 ^:, ) -chrM 6810 T T 25 0 25 1 , I -chrM 6811 A A 25 0 25 1 , I -chrM 6812 C C 5 0 25 1 , & -chrM 6813 A A 25 0 25 1 , I -chrM 6814 G G 25 0 25 1 , I -chrM 6815 T T 25 0 25 1 , I -chrM 6816 A A 25 0 25 1 , I -chrM 6817 G G 25 0 25 1 , I -chrM 6818 A A 25 0 25 1 , I -chrM 6819 A A 25 0 25 1 , I -chrM 6820 T T 25 0 25 1 , I -chrM 6821 T T 25 0 25 1 , I -chrM 6822 A A 25 0 25 1 , I -chrM 6823 A A 25 0 25 1 , I -chrM 6824 C C 16 0 25 1 , 1 -chrM 6825 C C 25 0 25 1 , I -chrM 6826 T T 25 0 25 1 , I -chrM 6827 C C 25 0 25 1 , I -chrM 6828 A A 25 0 25 1 , I -chrM 6829 A A 25 0 25 1 , I -chrM 6830 C C 25 0 25 1 , I -chrM 6831 T T 25 0 25 1 , I -chrM 6832 A A 25 0 25 1 , I -chrM 6833 A A 25 0 25 1 , I -chrM 6834 T T 25 0 25 1 , I -chrM 6835 C C 25 0 25 1 , I -chrM 6836 T A 4 4 25 1 n " -chrM 6837 G A 4 4 25 1 n " -chrM 6838 G G 25 0 25 1 , I -chrM 6839 A A 25 0 25 1 , I -chrM 6840 A A 25 0 25 1 , I -chrM 6841 T T 25 0 25 1 , I -chrM 6842 G G 25 0 25 1 , I -chrM 6843 A A 25 0 25 1 , I -chrM 6844 C C 25 0 25 1 ,$ I -chrM 7018 A A 25 0 25 1 ^:. I -chrM 7019 A A 25 0 25 1 . I -chrM 7020 A A 25 0 25 1 . I -chrM 7021 T T 25 0 25 1 . I -chrM 7022 T T 25 0 25 1 . I -chrM 7023 A A 25 0 25 1 . I -chrM 7024 T T 25 0 25 1 . I -chrM 7025 A A 4 0 25 1 N " -chrM 7026 G A 4 4 25 1 N " -chrM 7027 G G 25 0 25 1 . I -chrM 7028 T T 25 0 25 1 . I -chrM 7029 T T 25 0 25 1 . I -chrM 7030 A A 25 0 25 1 . I -chrM 7031 A A 25 0 25 1 . I -chrM 7032 A A 25 0 25 1 . I -chrM 7033 C C 25 0 25 1 . I -chrM 7034 C C 25 0 25 1 . I -chrM 7035 C C 25 0 25 1 . I -chrM 7036 C C 25 0 25 1 . I -chrM 7037 T T 25 0 25 1 . I -chrM 7038 A A 25 0 25 1 . I -chrM 7039 T T 25 0 25 1 . I -chrM 7040 A A 25 0 25 1 . B -chrM 7041 T T 25 0 25 1 . I -chrM 7042 A A 25 0 25 1 . D -chrM 7043 C C 25 0 25 1 . I -chrM 7044 C C 25 0 25 1 . I -chrM 7045 T T 25 0 25 1 . I -chrM 7046 C C 25 0 25 1 . I -chrM 7047 T T 25 0 25 1 . I -chrM 7048 A A 15 0 25 1 . 0 -chrM 7049 T T 25 0 25 1 . I -chrM 7050 G G 25 0 25 1 . I -chrM 7051 G G 12 0 25 1 . - -chrM 7052 C C 25 0 25 1 . I -chrM 7053 C C 25 0 25 1 .$ G -chrM 7122 C C 25 0 25 1 ^:, I -chrM 7123 C C 25 0 25 1 , I -chrM 7124 A A 25 0 25 1 , I -chrM 7125 C C 19 0 25 1 , 4 -chrM 7126 A A 25 0 25 1 , I -chrM 7127 C C 25 0 25 1 , I -chrM 7128 A A 25 0 25 1 , I -chrM 7129 C C 25 0 25 1 , I -chrM 7130 T T 25 0 25 1 , I -chrM 7131 A A 25 0 25 1 , I -chrM 7132 A A 25 0 25 1 , I -chrM 7133 T T 25 0 25 1 , I -chrM 7134 A A 25 0 25 1 , I -chrM 7135 A A 25 0 25 1 , I -chrM 7136 T T 25 0 25 1 , I -chrM 7137 C C 25 0 25 1 , I -chrM 7138 G G 25 0 25 1 , I -chrM 7139 T T 25 0 25 1 , I -chrM 7140 A A 25 0 25 1 , I -chrM 7141 T T 25 0 25 1 , I -chrM 7142 T T 25 0 25 1 , I -chrM 7143 C C 25 0 25 1 , I -chrM 7144 C C 25 0 25 1 , I -chrM 7145 T T 25 0 25 1 , I -chrM 7146 A A 25 0 25 1 , I -chrM 7147 A A 25 0 25 1 , I -chrM 7148 T T 25 0 25 1 , I -chrM 7149 T A 4 4 25 1 n " -chrM 7150 A A 4 0 25 1 n " -chrM 7151 G G 25 0 25 1 , I -chrM 7152 C C 25 0 25 1 , I -chrM 7153 T T 25 0 25 1 , I -chrM 7154 C C 25 0 25 1 , I -chrM 7155 T T 25 0 25 1 , I -chrM 7156 C C 25 0 25 1 , I -chrM 7157 T T 25 0 25 1 ,$ I -chrM 7191 T T 25 0 25 1 ^:, < -chrM 7192 A A 25 0 25 1 , I -chrM 7193 A A 25 0 25 1 , I -chrM 7194 A A 25 0 25 1 , I -chrM 7195 T T 15 0 25 1 , 0 -chrM 7196 T T 25 0 25 1 , E -chrM 7197 A A 25 0 25 1 , I -chrM 7198 A A 25 0 25 1 , I -chrM 7199 C C 18 0 25 1 , 3 -chrM 7200 C C 10 0 25 1 , + -chrM 7201 C C 18 0 25 1 , 3 -chrM 7202 A A 25 0 25 1 , I -chrM 7203 T T 17 0 25 1 , 2 -chrM 7204 A A 24 0 25 1 , 9 -chrM 7205 C C 25 0 25 1 , I -chrM 7206 C C 25 0 25 1 , > -chrM 7207 A A 25 0 25 1 , I -chrM 7208 G G 25 0 25 1 , I -chrM 7209 C C 25 0 25 1 , I -chrM 7210 A A 23 0 25 1 , 8 -chrM 7211 C C 25 0 25 1 , A -chrM 7212 C C 25 0 25 1 , I -chrM 7213 A A 25 0 25 1 , I -chrM 7214 T T 25 0 25 1 , I -chrM 7215 A A 25 0 25 1 , I -chrM 7216 G G 25 0 25 1 , I -chrM 7217 A A 25 0 25 1 , I -chrM 7218 T A 4 4 25 1 n " -chrM 7219 G A 4 4 25 1 n " -chrM 7220 C C 25 0 25 1 , I -chrM 7221 T T 25 0 25 1 , I -chrM 7222 C C 25 0 25 1 , I -chrM 7223 A A 25 0 25 1 , I -chrM 7224 A A 25 0 25 1 , I -chrM 7225 G G 25 0 25 1 , I -chrM 7226 A A 25 0 25 1 ,$ I -chrM 7348 G G 25 0 25 1 ^:, I -chrM 7349 G G 25 0 25 1 , I -chrM 7350 C C 14 0 25 1 , / -chrM 7351 C C 25 0 25 1 , < -chrM 7352 A A 8 0 25 1 , ) -chrM 7353 C C 17 0 25 1 , 2 -chrM 7354 C C 25 0 25 1 , I -chrM 7355 A A 25 0 25 1 , I -chrM 7356 A A 25 0 25 1 , I -chrM 7357 T T 25 0 25 1 , I -chrM 7358 G G 25 0 25 1 , I -chrM 7359 A A 25 0 25 1 , I -chrM 7360 T T 25 0 25 1 , I -chrM 7361 A A 25 0 25 1 , I -chrM 7362 C C 25 0 25 1 , I -chrM 7363 T T 25 0 25 1 , I -chrM 7364 G G 25 0 25 1 , I -chrM 7365 A A 25 0 25 1 , I -chrM 7366 A A 25 0 25 1 , I -chrM 7367 G G 25 0 25 1 , I -chrM 7368 C C 25 0 25 1 , I -chrM 7369 T T 25 0 25 1 , I -chrM 7370 A A 25 0 25 1 , I -chrM 7371 C C 25 0 25 1 , I -chrM 7372 G G 25 0 25 1 , I -chrM 7373 A A 25 0 25 1 , I -chrM 7374 G G 25 0 25 1 , I -chrM 7375 T A 4 4 25 1 n " -chrM 7376 A A 4 0 25 1 n " -chrM 7377 T T 25 0 25 1 , I -chrM 7378 A A 25 0 25 1 , I -chrM 7379 C C 25 0 25 1 , I -chrM 7380 C C 25 0 25 1 , I -chrM 7381 G G 25 0 25 1 , I -chrM 7382 A A 25 0 25 1 , I -chrM 7383 T T 25 0 25 1 ,$ I -chrM 7398 C C 25 0 25 1 ^:, I -chrM 7399 T T 25 0 25 1 , E -chrM 7400 T T 25 0 25 1 , I -chrM 7401 T T 25 0 25 1 , I -chrM 7402 G G 25 0 25 1 , I -chrM 7403 A A 25 0 25 1 , I -chrM 7404 C C 25 0 25 1 , I -chrM 7405 T T 25 0 25 1 , I -chrM 7406 C C 25 0 25 1 , I -chrM 7407 C C 25 0 25 1 , I -chrM 7408 T T 25 0 25 1 , I -chrM 7409 A A 25 0 25 1 , I -chrM 7410 C C 25 0 25 1 , I -chrM 7411 A A 25 0 25 1 , I -chrM 7412 T T 25 0 25 1 , I -chrM 7413 G G 25 0 25 1 , I -chrM 7414 A A 25 0 25 1 , I -chrM 7415 T T 25 0 25 1 , I -chrM 7416 C C 25 0 25 1 , I -chrM 7417 C C 25 0 25 1 , I -chrM 7418 C C 25 0 25 1 , I -chrM 7419 C C 25 0 25 1 , I -chrM 7420 A A 25 0 25 1 , I -chrM 7421 C C 25 0 25 1 , I -chrM 7422 A A 25 0 25 1 , I -chrM 7423 T T 25 0 25 1 , I -chrM 7424 C C 25 0 25 1 , I -chrM 7425 A A 4 0 25 1 n " -chrM 7426 G A 4 4 25 1 n " -chrM 7427 A A 25 0 25 1 , I -chrM 7428 C C 25 0 25 1 , I -chrM 7429 C C 25 0 25 1 , I -chrM 7430 T T 25 0 25 1 , I -chrM 7431 A A 25 0 25 1 , I -chrM 7432 A A 25 0 25 1 , I -chrM 7433 A A 25 0 25 1 ,$ I -chrM 7564 G G 20 0 25 1 ^:, 5 -chrM 7565 A A 25 0 25 1 , I -chrM 7566 C C 25 0 25 1 , I -chrM 7567 G G 25 0 25 1 , I -chrM 7568 C C 25 0 25 1 , @ -chrM 7569 T T 21 0 25 1 , 6 -chrM 7570 A A 25 0 25 1 , I -chrM 7571 T T 25 0 25 1 , I -chrM 7572 C C 25 0 25 1 , I -chrM 7573 C C 25 0 25 1 , I -chrM 7574 C C 25 0 25 1 , I -chrM 7575 T T 25 0 25 1 , > -chrM 7576 G G 25 0 25 1 , I -chrM 7577 G G 25 0 25 1 , I -chrM 7578 G G 25 0 25 1 , I -chrM 7579 C C 20 0 25 1 , 5 -chrM 7580 G G 25 0 25 1 , I -chrM 7581 C C 25 0 25 1 , I -chrM 7582 C C 25 0 25 1 , I -chrM 7583 T T 25 0 25 1 , I -chrM 7584 A A 25 0 25 1 , I -chrM 7585 A A 25 0 25 1 , I -chrM 7586 A A 25 0 25 1 , I -chrM 7587 T T 25 0 25 1 , I -chrM 7588 C C 25 0 25 1 , I -chrM 7589 A A 25 0 25 1 , I -chrM 7590 G G 25 0 25 1 , I -chrM 7591 A A 4 0 25 1 n " -chrM 7592 C A 4 4 25 1 n " -chrM 7593 A A 25 0 25 1 , I -chrM 7594 A A 25 0 25 1 , I -chrM 7595 C C 25 0 25 1 , I -chrM 7596 T T 25 0 25 1 , I -chrM 7597 C C 25 0 25 1 , I -chrM 7598 T T 25 0 25 1 , I -chrM 7599 C C 25 0 25 1 ,$ I -chrM 7752 A A 25 0 25 1 ^:. I -chrM 7753 G G 25 0 25 1 . I -chrM 7754 C C 25 0 25 1 . I -chrM 7755 A A 25 0 25 1 . I -chrM 7756 T T 25 0 25 1 . I -chrM 7757 T T 25 0 25 1 . I -chrM 7758 A A 25 0 25 1 . I -chrM 7759 A A 4 0 25 1 N " -chrM 7760 C A 4 4 25 1 N " -chrM 7761 C C 25 0 25 1 . I -chrM 7762 T T 25 0 25 1 . I -chrM 7763 T T 25 0 25 1 . I -chrM 7764 T T 25 0 25 1 . I -chrM 7765 T T 25 0 25 1 . I -chrM 7766 A A 25 0 25 1 . I -chrM 7767 A A 11 0 25 1 . , -chrM 7768 G G 25 0 25 1 . I -chrM 7769 T T 25 0 25 1 . I -chrM 7770 T T 25 0 25 1 . I -chrM 7771 A A 25 0 25 1 . B -chrM 7772 A A 25 0 25 1 . ; -chrM 7773 A A 25 0 25 1 . B -chrM 7774 G G 25 0 25 1 . I -chrM 7775 A A 25 0 25 1 . < -chrM 7776 T T 25 0 25 1 . I -chrM 7777 T T 25 0 25 1 . I -chrM 7778 G G 25 0 25 1 . I -chrM 7779 A A 25 0 25 1 . I -chrM 7780 G G 25 0 25 1 . I -chrM 7781 G G 25 0 25 1 . I -chrM 7782 G G 10 0 25 1 . + -chrM 7783 T T 25 0 25 1 . I -chrM 7784 T T 25 0 25 1 . I -chrM 7785 C C 25 0 25 1 . I -chrM 7786 A A 25 0 25 1 . B -chrM 7787 A A 25 0 25 1 .$ I -chrM 7971 G G 25 0 25 1 ^:, @ -chrM 7972 A A 25 0 25 1 , I -chrM 7973 A A 25 0 25 1 , I -chrM 7974 A A 25 0 25 1 , I -chrM 7975 A A 25 0 25 1 , I -chrM 7976 T T 22 0 25 1 , 7 -chrM 7977 C C 25 0 25 1 , I -chrM 7978 T T 25 0 25 1 , I -chrM 7979 A A 25 0 25 1 , I -chrM 7980 T T 25 0 25 1 , D -chrM 7981 T T 25 0 25 1 , C -chrM 7982 C C 25 0 25 1 , I -chrM 7983 G G 25 0 25 1 , I -chrM 7984 C C 25 0 25 1 , I -chrM 7985 C C 25 0 25 1 , I -chrM 7986 T T 25 0 25 1 , B -chrM 7987 C C 25 0 25 1 , I -chrM 7988 T T 25 0 25 1 , I -chrM 7989 T T 25 0 25 1 , I -chrM 7990 T T 25 0 25 1 , I -chrM 7991 C C 25 0 25 1 , I -chrM 7992 G G 25 0 25 1 , I -chrM 7993 C C 25 0 25 1 , I -chrM 7994 T T 25 0 25 1 , I -chrM 7995 A A 25 0 25 1 , I -chrM 7996 C C 25 0 25 1 , I -chrM 7997 C C 25 0 25 1 , I -chrM 7998 C A 4 4 25 1 n " -chrM 7999 C A 4 4 25 1 n " -chrM 8000 A A 25 0 25 1 , I -chrM 8001 A A 25 0 25 1 , I -chrM 8002 C C 25 0 25 1 , I -chrM 8003 A A 25 0 25 1 , I -chrM 8004 A A 25 0 25 1 , I -chrM 8005 T T 25 0 25 1 , I -chrM 8006 A A 25 0 25 1 ,$ I -chrM 8346 T T 25 0 25 1 ^:. I -chrM 8347 T T 25 0 25 1 . I -chrM 8348 T T 25 0 25 1 . I -chrM 8349 C C 25 0 25 1 . I -chrM 8350 T T 25 0 25 1 . I -chrM 8351 A A 25 0 25 1 . I -chrM 8352 C C 25 0 25 1 . I -chrM 8353 C A 4 4 25 1 N " -chrM 8354 T A 4 4 25 1 N " -chrM 8355 C C 25 0 25 1 . I -chrM 8356 A A 25 0 25 1 . I -chrM 8357 A A 25 0 25 1 . I -chrM 8358 G G 25 0 25 1 . I -chrM 8359 G G 25 0 25 1 . I -chrM 8360 G G 25 0 25 1 . = -chrM 8361 A A 25 0 25 1 . I -chrM 8362 C C 22 0 25 1 . 7 -chrM 8363 G G 25 0 25 1 . I -chrM 8364 C C 25 0 25 1 . I -chrM 8365 C C 25 0 25 1 . I -chrM 8366 C C 25 0 25 1 . I -chrM 8367 A A 18 0 25 1 . 3 -chrM 8368 T T 25 0 25 1 . I -chrM 8369 T T 25 0 25 1 . I -chrM 8370 T T 25 0 25 1 . I -chrM 8371 T T 25 0 25 1 . I -chrM 8372 C C 25 0 25 1 . I -chrM 8373 C C 25 0 25 1 . I -chrM 8374 T T 25 0 25 1 . I -chrM 8375 C C 25 0 25 1 . I -chrM 8376 A A 14 0 25 1 . / -chrM 8377 T T 25 0 25 1 . I -chrM 8378 C C 25 0 25 1 . D -chrM 8379 C C 25 0 25 1 . @ -chrM 8380 C C 25 0 25 1 . I -chrM 8381 C C 25 0 25 1 .$ I -chrM 8421 C C 25 0 25 1 ^:, I -chrM 8422 C C 25 0 25 1 , I -chrM 8423 T T 4 0 25 1 , % -chrM 8424 G G 25 0 25 1 , : -chrM 8425 T T 25 0 25 1 , : -chrM 8426 A A 25 0 25 1 , I -chrM 8427 G G 25 0 25 1 , < -chrM 8428 C C 25 0 25 1 , I -chrM 8429 C C 25 0 25 1 , I -chrM 8430 C C 25 0 25 1 , I -chrM 8431 T T 25 0 25 1 , I -chrM 8432 A A 25 0 25 1 , I -chrM 8433 G G 25 0 25 1 , E -chrM 8434 C C 25 0 25 1 , I -chrM 8435 C C 25 0 25 1 , I -chrM 8436 G G 25 0 25 1 , I -chrM 8437 T T 23 0 25 1 , 8 -chrM 8438 G G 25 0 25 1 , I -chrM 8439 C C 25 0 25 1 , I -chrM 8440 G G 25 0 25 1 , I -chrM 8441 G G 25 0 25 1 , I -chrM 8442 C C 25 0 25 1 , I -chrM 8443 T T 25 0 25 1 , I -chrM 8444 A A 25 0 25 1 , I -chrM 8445 A A 25 0 25 1 , I -chrM 8446 C C 25 0 25 1 , I -chrM 8447 C C 25 0 25 1 , I -chrM 8448 G A 4 4 25 1 n " -chrM 8449 C A 4 4 25 1 n " -chrM 8450 T T 33 0 25 2 ,^:, II +chrM 6730 G G 33 0 25 2 .$. >H +chrM 6731 G G 30 0 25 1 . I +chrM 6732 A A 30 0 25 1 . = +chrM 6733 T T 30 0 25 1 . I +chrM 6734 C C 30 0 25 1 . I +chrM 6735 T T 30 0 25 1 . E +chrM 6736 T T 30 0 25 1 . B +chrM 6737 T T 30 0 25 1 . A +chrM 6738 T T 30 0 25 1 .$ ? +chrM 6809 C N 0 0 0 1 ^:, ) +chrM 6810 T T 30 0 25 1 , I +chrM 6811 A A 30 0 25 1 , I +chrM 6812 C N 0 0 0 1 , & +chrM 6813 A A 30 0 25 1 , I +chrM 6814 G G 30 0 25 1 , I +chrM 6815 T T 30 0 25 1 , I +chrM 6816 A A 30 0 25 1 , I +chrM 6817 G G 30 0 25 1 , I +chrM 6818 A A 30 0 25 1 , I +chrM 6819 A A 30 0 25 1 , I +chrM 6820 T T 30 0 25 1 , I +chrM 6821 T T 30 0 25 1 , I +chrM 6822 A A 30 0 25 1 , I +chrM 6823 A A 30 0 25 1 , I +chrM 6824 C C 30 0 25 1 , 1 +chrM 6825 C C 30 0 25 1 , I +chrM 6826 T T 30 0 25 1 , I +chrM 6827 C C 30 0 25 1 , I +chrM 6828 A A 30 0 25 1 , I +chrM 6829 A A 30 0 25 1 , I +chrM 6830 C C 30 0 25 1 , I +chrM 6831 T T 30 0 25 1 , I +chrM 6832 A A 30 0 25 1 , I +chrM 6833 A A 30 0 25 1 , I +chrM 6834 T T 30 0 25 1 , I +chrM 6835 C C 30 0 25 1 , I +chrM 6836 T N 0 0 0 1 n " +chrM 6837 G N 0 0 0 1 n " +chrM 6838 G G 30 0 25 1 , I +chrM 6839 A A 30 0 25 1 , I +chrM 6840 A A 30 0 25 1 , I +chrM 6841 T T 30 0 25 1 , I +chrM 6842 G G 30 0 25 1 , I +chrM 6843 A A 30 0 25 1 , I +chrM 6844 C C 30 0 25 1 ,$ E +chrM 7018 A A 30 0 25 1 ^:. A +chrM 7019 A A 30 0 25 1 . B +chrM 7020 A A 30 0 25 1 . E +chrM 7021 T T 30 0 25 1 . I +chrM 7022 T T 30 0 25 1 . I +chrM 7023 A A 30 0 25 1 . I +chrM 7024 T T 30 0 25 1 . I +chrM 7025 A N 0 0 0 1 N " +chrM 7026 G N 0 0 0 1 N " +chrM 7027 G G 30 0 25 1 . I +chrM 7028 T T 30 0 25 1 . I +chrM 7029 T T 30 0 25 1 . I +chrM 7030 A A 30 0 25 1 . I +chrM 7031 A A 30 0 25 1 . I +chrM 7032 A A 30 0 25 1 . I +chrM 7033 C C 30 0 25 1 . I +chrM 7034 C C 30 0 25 1 . I +chrM 7035 C C 30 0 25 1 . I +chrM 7036 C C 30 0 25 1 . I +chrM 7037 T T 30 0 25 1 . I +chrM 7038 A A 30 0 25 1 . I +chrM 7039 T T 30 0 25 1 . I +chrM 7040 A A 30 0 25 1 . B +chrM 7041 T T 30 0 25 1 . I +chrM 7042 A A 30 0 25 1 . D +chrM 7043 C C 30 0 25 1 . I +chrM 7044 C C 30 0 25 1 . I +chrM 7045 T T 30 0 25 1 . I +chrM 7046 C C 30 0 25 1 . I +chrM 7047 T T 30 0 25 1 . I +chrM 7048 A A 30 0 25 1 . 0 +chrM 7049 T T 30 0 25 1 . I +chrM 7050 G G 30 0 25 1 . I +chrM 7051 G N 0 0 0 1 . - +chrM 7052 C C 30 0 25 1 . E +chrM 7053 C C 30 0 25 1 .$ B +chrM 7122 C C 30 0 25 1 ^:, B +chrM 7123 C C 30 0 25 1 , E +chrM 7124 A A 30 0 25 1 , I +chrM 7125 C C 30 0 25 1 , 4 +chrM 7126 A A 30 0 25 1 , I +chrM 7127 C C 30 0 25 1 , I +chrM 7128 A A 30 0 25 1 , I +chrM 7129 C C 30 0 25 1 , I +chrM 7130 T T 30 0 25 1 , I +chrM 7131 A A 30 0 25 1 , I +chrM 7132 A A 30 0 25 1 , I +chrM 7133 T T 30 0 25 1 , I +chrM 7134 A A 30 0 25 1 , I +chrM 7135 A A 30 0 25 1 , I +chrM 7136 T T 30 0 25 1 , I +chrM 7137 C C 30 0 25 1 , I +chrM 7138 G G 30 0 25 1 , I +chrM 7139 T T 30 0 25 1 , I +chrM 7140 A A 30 0 25 1 , I +chrM 7141 T T 30 0 25 1 , I +chrM 7142 T T 30 0 25 1 , I +chrM 7143 C C 30 0 25 1 , I +chrM 7144 C C 30 0 25 1 , I +chrM 7145 T T 30 0 25 1 , I +chrM 7146 A A 30 0 25 1 , I +chrM 7147 A A 30 0 25 1 , I +chrM 7148 T T 30 0 25 1 , I +chrM 7149 T N 0 0 0 1 n " +chrM 7150 A N 0 0 0 1 n " +chrM 7151 G G 30 0 25 1 , I +chrM 7152 C C 30 0 25 1 , I +chrM 7153 T T 30 0 25 1 , I +chrM 7154 C C 30 0 25 1 , I +chrM 7155 T T 30 0 25 1 , I +chrM 7156 C C 30 0 25 1 , I +chrM 7157 T T 30 0 25 1 ,$ D +chrM 7191 T T 30 0 25 1 ^:, < +chrM 7192 A A 30 0 25 1 , I +chrM 7193 A A 30 0 25 1 , I +chrM 7194 A A 30 0 25 1 , I +chrM 7195 T T 30 0 25 1 , 0 +chrM 7196 T T 30 0 25 1 , E +chrM 7197 A A 30 0 25 1 , I +chrM 7198 A A 30 0 25 1 , I +chrM 7199 C C 30 0 25 1 , 3 +chrM 7200 C N 0 0 0 1 , + +chrM 7201 C C 30 0 25 1 , 3 +chrM 7202 A A 30 0 25 1 , I +chrM 7203 T T 30 0 25 1 , 2 +chrM 7204 A A 30 0 25 1 , 9 +chrM 7205 C C 30 0 25 1 , I +chrM 7206 C C 30 0 25 1 , > +chrM 7207 A A 30 0 25 1 , I +chrM 7208 G G 30 0 25 1 , I +chrM 7209 C C 30 0 25 1 , I +chrM 7210 A A 30 0 25 1 , 8 +chrM 7211 C C 30 0 25 1 , A +chrM 7212 C C 30 0 25 1 , I +chrM 7213 A A 30 0 25 1 , I +chrM 7214 T T 30 0 25 1 , I +chrM 7215 A A 30 0 25 1 , I +chrM 7216 G G 30 0 25 1 , I +chrM 7217 A A 30 0 25 1 , I +chrM 7218 T N 0 0 0 1 n " +chrM 7219 G N 0 0 0 1 n " +chrM 7220 C C 30 0 25 1 , I +chrM 7221 T T 30 0 25 1 , I +chrM 7222 C C 30 0 25 1 , I +chrM 7223 A A 30 0 25 1 , I +chrM 7224 A A 30 0 25 1 , I +chrM 7225 G G 30 0 25 1 , I +chrM 7226 A A 30 0 25 1 ,$ > +chrM 7348 G G 30 0 25 1 ^:, B +chrM 7349 G G 30 0 25 1 , E +chrM 7350 C C 30 0 25 1 , / +chrM 7351 C C 30 0 25 1 , < +chrM 7352 A N 0 0 0 1 , ) +chrM 7353 C C 30 0 25 1 , 2 +chrM 7354 C C 30 0 25 1 , I +chrM 7355 A A 30 0 25 1 , I +chrM 7356 A A 30 0 25 1 , I +chrM 7357 T T 30 0 25 1 , I +chrM 7358 G G 30 0 25 1 , I +chrM 7359 A A 30 0 25 1 , I +chrM 7360 T T 30 0 25 1 , I +chrM 7361 A A 30 0 25 1 , I +chrM 7362 C C 30 0 25 1 , I +chrM 7363 T T 30 0 25 1 , I +chrM 7364 G G 30 0 25 1 , I +chrM 7365 A A 30 0 25 1 , I +chrM 7366 A A 30 0 25 1 , I +chrM 7367 G G 30 0 25 1 , I +chrM 7368 C C 30 0 25 1 , I +chrM 7369 T T 30 0 25 1 , I +chrM 7370 A A 30 0 25 1 , I +chrM 7371 C C 30 0 25 1 , I +chrM 7372 G G 30 0 25 1 , I +chrM 7373 A A 30 0 25 1 , I +chrM 7374 G G 30 0 25 1 , I +chrM 7375 T N 0 0 0 1 n " +chrM 7376 A N 0 0 0 1 n " +chrM 7377 T T 30 0 25 1 , I +chrM 7378 A A 30 0 25 1 , I +chrM 7379 C C 30 0 25 1 , I +chrM 7380 C C 30 0 25 1 , I +chrM 7381 G G 30 0 25 1 , I +chrM 7382 A A 30 0 25 1 , I +chrM 7383 T T 30 0 25 1 ,$ > +chrM 7398 C C 30 0 25 1 ^:, E +chrM 7399 T T 30 0 25 1 , E +chrM 7400 T T 30 0 25 1 , I +chrM 7401 T T 30 0 25 1 , I +chrM 7402 G G 30 0 25 1 , I +chrM 7403 A A 30 0 25 1 , I +chrM 7404 C C 30 0 25 1 , I +chrM 7405 T T 30 0 25 1 , I +chrM 7406 C C 30 0 25 1 , I +chrM 7407 C C 30 0 25 1 , I +chrM 7408 T T 30 0 25 1 , I +chrM 7409 A A 30 0 25 1 , I +chrM 7410 C C 30 0 25 1 , I +chrM 7411 A A 30 0 25 1 , I +chrM 7412 T T 30 0 25 1 , I +chrM 7413 G G 30 0 25 1 , I +chrM 7414 A A 30 0 25 1 , I +chrM 7415 T T 30 0 25 1 , I +chrM 7416 C C 30 0 25 1 , I +chrM 7417 C C 30 0 25 1 , I +chrM 7418 C C 30 0 25 1 , I +chrM 7419 C C 30 0 25 1 , I +chrM 7420 A A 30 0 25 1 , I +chrM 7421 C C 30 0 25 1 , I +chrM 7422 A A 30 0 25 1 , I +chrM 7423 T T 30 0 25 1 , I +chrM 7424 C C 30 0 25 1 , I +chrM 7425 A N 0 0 0 1 n " +chrM 7426 G N 0 0 0 1 n " +chrM 7427 A A 30 0 25 1 , I +chrM 7428 C C 30 0 25 1 , I +chrM 7429 C C 30 0 25 1 , I +chrM 7430 T T 30 0 25 1 , I +chrM 7431 A A 30 0 25 1 , > +chrM 7432 A A 30 0 25 1 , ; +chrM 7433 A A 30 0 25 1 ,$ : +chrM 7564 G G 30 0 25 1 ^:, 5 +chrM 7565 A A 30 0 25 1 , I +chrM 7566 C C 30 0 25 1 , I +chrM 7567 G G 30 0 25 1 , I +chrM 7568 C C 30 0 25 1 , @ +chrM 7569 T T 30 0 25 1 , 6 +chrM 7570 A A 30 0 25 1 , I +chrM 7571 T T 30 0 25 1 , I +chrM 7572 C C 30 0 25 1 , I +chrM 7573 C C 30 0 25 1 , I +chrM 7574 C C 30 0 25 1 , I +chrM 7575 T T 30 0 25 1 , > +chrM 7576 G G 30 0 25 1 , I +chrM 7577 G G 30 0 25 1 , I +chrM 7578 G G 30 0 25 1 , I +chrM 7579 C C 30 0 25 1 , 5 +chrM 7580 G G 30 0 25 1 , I +chrM 7581 C C 30 0 25 1 , I +chrM 7582 C C 30 0 25 1 , I +chrM 7583 T T 30 0 25 1 , I +chrM 7584 A A 30 0 25 1 , I +chrM 7585 A A 30 0 25 1 , I +chrM 7586 A A 30 0 25 1 , I +chrM 7587 T T 30 0 25 1 , I +chrM 7588 C C 30 0 25 1 , I +chrM 7589 A A 30 0 25 1 , I +chrM 7590 G G 30 0 25 1 , I +chrM 7591 A N 0 0 0 1 n " +chrM 7592 C N 0 0 0 1 n " +chrM 7593 A A 30 0 25 1 , I +chrM 7594 A A 30 0 25 1 , I +chrM 7595 C C 30 0 25 1 , I +chrM 7596 T T 30 0 25 1 , I +chrM 7597 C C 30 0 25 1 , I +chrM 7598 T T 30 0 25 1 , I +chrM 7599 C C 30 0 25 1 ,$ E +chrM 7752 A A 30 0 25 1 ^:. E +chrM 7753 G G 30 0 25 1 . I +chrM 7754 C C 30 0 25 1 . I +chrM 7755 A A 30 0 25 1 . I +chrM 7756 T T 30 0 25 1 . I +chrM 7757 T T 30 0 25 1 . I +chrM 7758 A A 30 0 25 1 . I +chrM 7759 A N 0 0 0 1 N " +chrM 7760 C N 0 0 0 1 N " +chrM 7761 C C 30 0 25 1 . I +chrM 7762 T T 30 0 25 1 . I +chrM 7763 T T 30 0 25 1 . I +chrM 7764 T T 30 0 25 1 . I +chrM 7765 T T 30 0 25 1 . I +chrM 7766 A A 30 0 25 1 . I +chrM 7767 A N 0 0 0 1 . , +chrM 7768 G G 30 0 25 1 . I +chrM 7769 T T 30 0 25 1 . I +chrM 7770 T T 30 0 25 1 . I +chrM 7771 A A 30 0 25 1 . B +chrM 7772 A A 30 0 25 1 . ; +chrM 7773 A A 30 0 25 1 . B +chrM 7774 G G 30 0 25 1 . I +chrM 7775 A A 30 0 25 1 . < +chrM 7776 T T 30 0 25 1 . I +chrM 7777 T T 30 0 25 1 . I +chrM 7778 G G 30 0 25 1 . I +chrM 7779 A A 30 0 25 1 . I +chrM 7780 G G 30 0 25 1 . I +chrM 7781 G G 30 0 25 1 . I +chrM 7782 G N 0 0 0 1 . + +chrM 7783 T T 30 0 25 1 . I +chrM 7784 T T 30 0 25 1 . I +chrM 7785 C C 30 0 25 1 . I +chrM 7786 A A 30 0 25 1 . B +chrM 7787 A A 30 0 25 1 .$ B +chrM 7971 G G 30 0 25 1 ^:, @ +chrM 7972 A A 30 0 25 1 , I +chrM 7973 A A 30 0 25 1 , I +chrM 7974 A A 30 0 25 1 , I +chrM 7975 A A 30 0 25 1 , I +chrM 7976 T T 30 0 25 1 , 7 +chrM 7977 C C 30 0 25 1 , I +chrM 7978 T T 30 0 25 1 , I +chrM 7979 A A 30 0 25 1 , I +chrM 7980 T T 30 0 25 1 , D +chrM 7981 T T 30 0 25 1 , C +chrM 7982 C C 30 0 25 1 , I +chrM 7983 G G 30 0 25 1 , I +chrM 7984 C C 30 0 25 1 , I +chrM 7985 C C 30 0 25 1 , I +chrM 7986 T T 30 0 25 1 , B +chrM 7987 C C 30 0 25 1 , I +chrM 7988 T T 30 0 25 1 , I +chrM 7989 T T 30 0 25 1 , I +chrM 7990 T T 30 0 25 1 , I +chrM 7991 C C 30 0 25 1 , I +chrM 7992 G G 30 0 25 1 , I +chrM 7993 C C 30 0 25 1 , I +chrM 7994 T T 30 0 25 1 , I +chrM 7995 A A 30 0 25 1 , I +chrM 7996 C C 30 0 25 1 , I +chrM 7997 C C 30 0 25 1 , I +chrM 7998 C N 0 0 0 1 n " +chrM 7999 C N 0 0 0 1 n " +chrM 8000 A A 30 0 25 1 , I +chrM 8001 A A 30 0 25 1 , I +chrM 8002 C C 30 0 25 1 , I +chrM 8003 A A 30 0 25 1 , I +chrM 8004 A A 30 0 25 1 , I +chrM 8005 T T 30 0 25 1 , I +chrM 8006 A A 30 0 25 1 ,$ E +chrM 8346 T T 30 0 25 1 ^:. A +chrM 8347 T T 30 0 25 1 . B +chrM 8348 T T 30 0 25 1 . E +chrM 8349 C C 30 0 25 1 . I +chrM 8350 T T 30 0 25 1 . I +chrM 8351 A A 30 0 25 1 . I +chrM 8352 C C 30 0 25 1 . I +chrM 8353 C N 0 0 0 1 N " +chrM 8354 T N 0 0 0 1 N " +chrM 8355 C C 30 0 25 1 . I +chrM 8356 A A 30 0 25 1 . I +chrM 8357 A A 30 0 25 1 . I +chrM 8358 G G 30 0 25 1 . I +chrM 8359 G G 30 0 25 1 . I +chrM 8360 G G 30 0 25 1 . = +chrM 8361 A A 30 0 25 1 . I +chrM 8362 C C 30 0 25 1 . 7 +chrM 8363 G G 30 0 25 1 . I +chrM 8364 C C 30 0 25 1 . I +chrM 8365 C C 30 0 25 1 . I +chrM 8366 C C 30 0 25 1 . I +chrM 8367 A A 30 0 25 1 . 3 +chrM 8368 T T 30 0 25 1 . I +chrM 8369 T T 30 0 25 1 . I +chrM 8370 T T 30 0 25 1 . I +chrM 8371 T T 30 0 25 1 . I +chrM 8372 C C 30 0 25 1 . I +chrM 8373 C C 30 0 25 1 . I +chrM 8374 T T 30 0 25 1 . I +chrM 8375 C C 30 0 25 1 . I +chrM 8376 A A 30 0 25 1 . / +chrM 8377 T T 30 0 25 1 . I +chrM 8378 C C 30 0 25 1 . D +chrM 8379 C C 30 0 25 1 . @ +chrM 8380 C C 30 0 25 1 . A +chrM 8381 C C 30 0 25 1 .$ ? +chrM 8421 C C 30 0 25 1 ^:, B +chrM 8422 C C 30 0 25 1 , E +chrM 8423 T N 0 0 0 1 , % +chrM 8424 G G 30 0 25 1 , : +chrM 8425 T T 30 0 25 1 , : +chrM 8426 A A 30 0 25 1 , I +chrM 8427 G G 30 0 25 1 , < +chrM 8428 C C 30 0 25 1 , I +chrM 8429 C C 30 0 25 1 , I +chrM 8430 C C 30 0 25 1 , I +chrM 8431 T T 30 0 25 1 , I +chrM 8432 A A 30 0 25 1 , I +chrM 8433 G G 30 0 25 1 , E +chrM 8434 C C 30 0 25 1 , I +chrM 8435 C C 30 0 25 1 , I +chrM 8436 G G 30 0 25 1 , I +chrM 8437 T T 30 0 25 1 , 8 +chrM 8438 G G 30 0 25 1 , I +chrM 8439 C C 30 0 25 1 , I +chrM 8440 G G 30 0 25 1 , I +chrM 8441 G G 30 0 25 1 , I +chrM 8442 C C 30 0 25 1 , I +chrM 8443 T T 30 0 25 1 , I +chrM 8444 A A 30 0 25 1 , I +chrM 8445 A A 30 0 25 1 , I +chrM 8446 C C 30 0 25 1 , I +chrM 8447 C C 30 0 25 1 , I +chrM 8448 G N 0 0 0 1 n " +chrM 8449 C N 0 0 0 1 n " +chrM 8450 T T 33 0 25 2 ,^:, IE chrM 8451 A A 33 0 25 2 ,, II chrM 8452 A A 33 0 25 2 ,, II chrM 8453 C C 33 0 25 2 ,, II chrM 8454 A A 33 0 25 2 ,, II -chrM 8455 T T 33 0 25 2 ,, I> -chrM 8456 T T 33 0 25 2 ,$, I1 -chrM 8457 A A 25 0 25 1 , I -chrM 8458 C C 25 0 25 1 , I -chrM 8459 C C 25 0 25 1 , I -chrM 8460 G G 25 0 25 1 , I -chrM 8461 C C 25 0 25 1 , I -chrM 8462 C C 25 0 25 1 , I -chrM 8463 G G 25 0 25 1 , I -chrM 8464 G G 25 0 25 1 , I -chrM 8465 A A 25 0 25 1 , I -chrM 8466 C C 25 0 25 1 , I -chrM 8467 A A 25 0 25 1 , I -chrM 8468 C C 25 0 25 1 , I -chrM 8469 C C 25 0 25 1 , I -chrM 8470 T T 25 0 25 1 , I -chrM 8471 C C 25 0 25 1 , I -chrM 8472 C C 25 0 25 1 , I -chrM 8473 T T 25 0 25 1 , I -chrM 8474 A A 25 0 25 1 , I -chrM 8475 A A 25 0 25 1 , I -chrM 8476 T T 25 0 25 1 , I -chrM 8477 A A 4 0 25 1 n " -chrM 8478 C A 4 4 25 1 n " -chrM 8479 A A 25 0 25 1 , I -chrM 8480 C C 25 0 25 1 , I -chrM 8481 C C 25 0 25 1 , I -chrM 8482 T T 25 0 25 1 , I -chrM 8483 C C 25 0 25 1 , I -chrM 8484 A A 25 0 25 1 , I -chrM 8485 T T 25 0 25 1 ,$ I -chrM 8630 A A 25 0 25 1 ^:. I -chrM 8631 C C 25 0 25 1 . I -chrM 8632 A A 25 0 25 1 . I -chrM 8633 C C 25 0 25 1 . I -chrM 8634 G G 25 0 25 1 . I -chrM 8635 A A 25 0 25 1 . I -chrM 8636 C C 25 0 25 1 . I -chrM 8637 A A 4 0 25 1 N " -chrM 8638 A A 4 0 25 1 N " -chrM 8639 C C 25 0 25 1 . I -chrM 8640 A A 25 0 25 1 . I -chrM 8641 C C 25 0 25 1 . I -chrM 8642 C C 25 0 25 1 . I -chrM 8643 T T 25 0 25 1 . I -chrM 8644 A A 25 0 25 1 . I -chrM 8645 A A 25 0 25 1 . I -chrM 8646 T T 25 0 25 1 . I -chrM 8647 G G 25 0 25 1 . I -chrM 8648 A A 25 0 25 1 . I -chrM 8649 C C 25 0 25 1 . I -chrM 8650 C C 25 0 25 1 . I -chrM 8651 C C 25 0 25 1 . I -chrM 8652 A A 25 0 25 1 . I -chrM 8653 C C 25 0 25 1 . I -chrM 8654 C C 25 0 25 1 . I -chrM 8655 A A 25 0 25 1 . > -chrM 8656 A A 25 0 25 1 . C -chrM 8657 A A 25 0 25 1 . : -chrM 8658 C C 25 0 25 1 . I -chrM 8659 C C 25 0 25 1 . I -chrM 8660 C C 25 0 25 1 . I -chrM 8661 A A 25 0 25 1 . D -chrM 8662 C C 25 0 25 1 . I -chrM 8663 G G 25 0 25 1 . < -chrM 8664 C C 25 0 25 1 . I -chrM 8665 T T 25 0 25 1 .$ I -chrM 8752 C C 25 0 25 1 ^:, I -chrM 8753 T T 25 0 25 1 , B -chrM 8754 T T 25 0 25 1 , I -chrM 8755 T T 25 0 25 1 , I -chrM 8756 A A 25 0 25 1 , I -chrM 8757 A A 25 0 25 1 , I -chrM 8758 C C 25 0 25 1 , I -chrM 8759 T T 25 0 25 1 , I -chrM 8760 C C 25 0 25 1 , I -chrM 8761 A A 25 0 25 1 , I -chrM 8762 A A 25 0 25 1 , I -chrM 8763 C C 25 0 25 1 , I -chrM 8764 C C 33 0 25 2 ,^:, II +chrM 8455 T T 33 0 25 2 ,, E> +chrM 8456 T T 33 0 25 2 ,$, B1 +chrM 8457 A A 30 0 25 1 , I +chrM 8458 C C 30 0 25 1 , I +chrM 8459 C C 30 0 25 1 , I +chrM 8460 G G 30 0 25 1 , I +chrM 8461 C C 30 0 25 1 , I +chrM 8462 C C 30 0 25 1 , I +chrM 8463 G G 30 0 25 1 , I +chrM 8464 G G 30 0 25 1 , I +chrM 8465 A A 30 0 25 1 , I +chrM 8466 C C 30 0 25 1 , I +chrM 8467 A A 30 0 25 1 , I +chrM 8468 C C 30 0 25 1 , I +chrM 8469 C C 30 0 25 1 , I +chrM 8470 T T 30 0 25 1 , I +chrM 8471 C C 30 0 25 1 , I +chrM 8472 C C 30 0 25 1 , I +chrM 8473 T T 30 0 25 1 , I +chrM 8474 A A 30 0 25 1 , I +chrM 8475 A A 30 0 25 1 , I +chrM 8476 T T 30 0 25 1 , I +chrM 8477 A N 0 0 0 1 n " +chrM 8478 C N 0 0 0 1 n " +chrM 8479 A A 30 0 25 1 , I +chrM 8480 C C 30 0 25 1 , I +chrM 8481 C C 30 0 25 1 , I +chrM 8482 T T 30 0 25 1 , I +chrM 8483 C C 30 0 25 1 , I +chrM 8484 A A 30 0 25 1 , I +chrM 8485 T T 30 0 25 1 ,$ E +chrM 8630 A A 30 0 25 1 ^:. E +chrM 8631 C C 30 0 25 1 . I +chrM 8632 A A 30 0 25 1 . I +chrM 8633 C C 30 0 25 1 . I +chrM 8634 G G 30 0 25 1 . I +chrM 8635 A A 30 0 25 1 . I +chrM 8636 C C 30 0 25 1 . I +chrM 8637 A N 0 0 0 1 N " +chrM 8638 A N 0 0 0 1 N " +chrM 8639 C C 30 0 25 1 . I +chrM 8640 A A 30 0 25 1 . I +chrM 8641 C C 30 0 25 1 . I +chrM 8642 C C 30 0 25 1 . I +chrM 8643 T T 30 0 25 1 . I +chrM 8644 A A 30 0 25 1 . I +chrM 8645 A A 30 0 25 1 . I +chrM 8646 T T 30 0 25 1 . I +chrM 8647 G G 30 0 25 1 . I +chrM 8648 A A 30 0 25 1 . I +chrM 8649 C C 30 0 25 1 . I +chrM 8650 C C 30 0 25 1 . I +chrM 8651 C C 30 0 25 1 . I +chrM 8652 A A 30 0 25 1 . I +chrM 8653 C C 30 0 25 1 . I +chrM 8654 C C 30 0 25 1 . I +chrM 8655 A A 30 0 25 1 . > +chrM 8656 A A 30 0 25 1 . C +chrM 8657 A A 30 0 25 1 . : +chrM 8658 C C 30 0 25 1 . I +chrM 8659 C C 30 0 25 1 . I +chrM 8660 C C 30 0 25 1 . I +chrM 8661 A A 30 0 25 1 . D +chrM 8662 C C 30 0 25 1 . I +chrM 8663 G G 30 0 25 1 . < +chrM 8664 C C 30 0 25 1 . I +chrM 8665 T T 30 0 25 1 .$ > +chrM 8752 C C 30 0 25 1 ^:, E +chrM 8753 T T 30 0 25 1 , B +chrM 8754 T T 30 0 25 1 , I +chrM 8755 T T 30 0 25 1 , I +chrM 8756 A A 30 0 25 1 , I +chrM 8757 A A 30 0 25 1 , I +chrM 8758 C C 30 0 25 1 , I +chrM 8759 T T 30 0 25 1 , I +chrM 8760 C C 30 0 25 1 , I +chrM 8761 A A 30 0 25 1 , I +chrM 8762 A A 30 0 25 1 , I +chrM 8763 C C 30 0 25 1 , I +chrM 8764 C C 33 0 25 2 ,^:, IE chrM 8765 T T 33 0 25 2 ,, IA chrM 8766 T T 33 0 25 2 ,, IA chrM 8767 A A 33 0 25 2 ,, II @@ -1684,593 +1684,593 @@ chrM 8775 C C 33 0 25 2 ,, II chrM 8776 T T 33 0 25 2 ,, II chrM 8777 A A 33 0 25 2 ,, II chrM 8778 T T 33 0 25 2 ,, II -chrM 8779 A A 28 0 25 2 n, "I -chrM 8780 G G 19 0 25 2 n, "I +chrM 8779 A A 30 0 25 2 n, "I +chrM 8780 G G 30 0 25 2 n, "I chrM 8781 G G 33 0 25 2 ,, II chrM 8782 G G 33 0 25 2 ,, II chrM 8783 C C 33 0 25 2 ,, II chrM 8784 T T 33 0 25 2 ,, II chrM 8785 A A 33 0 25 2 ,, II -chrM 8786 T T 33 0 25 2 ,, II -chrM 8787 T T 33 0 25 2 ,$, II -chrM 8788 A A 25 0 25 1 , I -chrM 8789 A A 25 0 25 1 , I -chrM 8790 C C 25 0 25 1 , I -chrM 8791 T A 4 4 25 1 n " -chrM 8792 A A 4 0 25 1 n " -chrM 8793 A A 25 0 25 1 , I -chrM 8794 C C 25 0 25 1 , I -chrM 8795 A A 25 0 25 1 , I -chrM 8796 T T 25 0 25 1 , I -chrM 8797 C C 25 0 25 1 , I -chrM 8798 C C 25 0 25 1 , I -chrM 8799 T T 25 0 25 1 ,$ I -chrM 8908 C C 25 0 25 1 ^:, I -chrM 8909 T T 25 0 25 1 , : -chrM 8910 C C 25 0 25 1 , I -chrM 8911 A A 25 0 25 1 , I -chrM 8912 G G 25 0 25 1 , D -chrM 8913 A A 25 0 25 1 , I -chrM 8914 A A 25 0 25 1 , I -chrM 8915 G G 25 0 25 1 , I -chrM 8916 T T 25 0 25 1 , I -chrM 8917 C C 25 0 25 1 , I -chrM 8918 T T 25 0 25 1 , I -chrM 8919 T T 25 0 25 1 , < -chrM 8920 C C 25 0 25 1 , I -chrM 8921 T T 25 0 25 1 , F -chrM 8922 T T 25 0 25 1 , I -chrM 8923 C C 25 0 25 1 , I -chrM 8924 T T 25 0 25 1 , F -chrM 8925 T T 25 0 25 1 , E -chrM 8926 C C 25 0 25 1 , I -chrM 8927 T T 25 0 25 1 , H -chrM 8928 C C 25 0 25 1 , I -chrM 8929 T T 33 0 25 2 ,^:, II +chrM 8786 T T 33 0 25 2 ,, EI +chrM 8787 T T 33 0 25 2 ,$, BI +chrM 8788 A A 30 0 25 1 , I +chrM 8789 A A 30 0 25 1 , I +chrM 8790 C C 30 0 25 1 , I +chrM 8791 T N 0 0 0 1 n " +chrM 8792 A N 0 0 0 1 n " +chrM 8793 A A 30 0 25 1 , I +chrM 8794 C C 30 0 25 1 , I +chrM 8795 A A 30 0 25 1 , I +chrM 8796 T T 30 0 25 1 , I +chrM 8797 C C 30 0 25 1 , I +chrM 8798 C C 30 0 25 1 , I +chrM 8799 T T 30 0 25 1 ,$ > +chrM 8908 C C 30 0 25 1 ^:, E +chrM 8909 T T 30 0 25 1 , : +chrM 8910 C C 30 0 25 1 , I +chrM 8911 A A 30 0 25 1 , I +chrM 8912 G G 30 0 25 1 , D +chrM 8913 A A 30 0 25 1 , I +chrM 8914 A A 30 0 25 1 , I +chrM 8915 G G 30 0 25 1 , I +chrM 8916 T T 30 0 25 1 , I +chrM 8917 C C 30 0 25 1 , I +chrM 8918 T T 30 0 25 1 , I +chrM 8919 T T 30 0 25 1 , < +chrM 8920 C C 30 0 25 1 , I +chrM 8921 T T 30 0 25 1 , F +chrM 8922 T T 30 0 25 1 , I +chrM 8923 C C 30 0 25 1 , I +chrM 8924 T T 30 0 25 1 , F +chrM 8925 T T 30 0 25 1 , E +chrM 8926 C C 30 0 25 1 , I +chrM 8927 T T 30 0 25 1 , H +chrM 8928 C C 30 0 25 1 , I +chrM 8929 T T 33 0 25 2 ,^:, IE chrM 8930 G G 33 0 25 2 ,, II chrM 8931 G G 33 0 25 2 ,, II chrM 8932 C C 33 0 25 2 ,, II chrM 8933 T T 33 0 25 2 ,, II chrM 8934 T T 33 0 25 2 ,, II -chrM 8935 C C 19 0 25 2 n, "I -chrM 8936 T T 19 0 25 2 n, "; +chrM 8935 C C 30 0 25 2 n, "I +chrM 8936 T T 30 0 25 2 n, "; chrM 8937 T T 33 0 25 2 ,, IG chrM 8938 C C 33 0 25 2 ,, II chrM 8939 T T 33 0 25 2 ,, IE chrM 8940 G G 33 0 25 2 ,, II chrM 8941 A A 33 0 25 2 ,, II chrM 8942 G G 33 0 25 2 ,, II -chrM 8943 C C 33 0 25 2 ,$, II -chrM 8944 C C 25 0 25 1 , I -chrM 8945 T T 25 0 25 1 , I -chrM 8946 T T 25 0 25 1 , I -chrM 8947 T T 25 0 25 1 , I -chrM 8948 T T 25 0 25 1 , I -chrM 8949 A A 25 0 25 1 , I -chrM 8950 C C 25 0 25 1 , I -chrM 8951 C C 25 0 25 1 , I -chrM 8952 A A 25 0 25 1 , I -chrM 8953 C C 25 0 25 1 , I -chrM 8954 T T 25 0 25 1 , I -chrM 8955 C C 25 0 25 1 , I -chrM 8956 A A 4 0 25 1 n " -chrM 8957 A A 4 0 25 1 n " -chrM 8958 G G 25 0 25 1 , I -chrM 8959 C C 25 0 25 1 , I -chrM 8960 C C 25 0 25 1 , I -chrM 8961 T T 25 0 25 1 , I -chrM 8962 A A 25 0 25 1 , I -chrM 8963 G G 25 0 25 1 , I -chrM 8964 C C 25 0 25 1 ,$ I -chrM 9111 G G 25 0 25 1 ^:. I -chrM 9112 T T 25 0 25 1 . I -chrM 9113 A A 25 0 25 1 . I -chrM 9114 A A 25 0 25 1 . I -chrM 9115 A A 25 0 25 1 . I -chrM 9116 A A 25 0 25 1 . I -chrM 9117 A A 25 0 25 1 . I -chrM 9118 T A 4 4 25 1 N " -chrM 9119 A A 4 0 25 1 N " -chrM 9120 T T 25 0 25 1 . I -chrM 9121 G G 25 0 25 1 . I -chrM 9122 C C 25 0 25 1 . I -chrM 9123 T T 25 0 25 1 . I -chrM 9124 C C 25 0 25 1 . I -chrM 9125 C C 25 0 25 1 . I -chrM 9126 A A 25 0 25 1 . I -chrM 9127 A A 25 0 25 1 . I -chrM 9128 G G 25 0 25 1 . I -chrM 9129 G G 25 0 25 1 . I -chrM 9130 C C 25 0 25 1 . I -chrM 9131 C C 25 0 25 1 . I -chrM 9132 T T 25 0 25 1 . I -chrM 9133 A A 25 0 25 1 . I -chrM 9134 T T 25 0 25 1 . I -chrM 9135 T T 25 0 25 1 . I -chrM 9136 C C 25 0 25 1 . I -chrM 9137 A A 25 0 25 1 . I -chrM 9138 T T 25 0 25 1 . I -chrM 9139 C C 25 0 25 1 . I -chrM 9140 A A 25 0 25 1 . E -chrM 9141 C C 25 0 25 1 . I -chrM 9142 A A 25 0 25 1 . B -chrM 9143 A A 23 0 25 1 . 8 -chrM 9144 T T 25 0 25 1 . I -chrM 9145 T T 25 0 25 1 . I -chrM 9146 T T 25 0 25 1 .$ I -chrM 9331 C C 5 0 25 1 ^:, & -chrM 9332 A A 11 0 25 1 , , -chrM 9333 G G 9 0 25 1 , * -chrM 9334 C C 25 0 25 1 , I -chrM 9335 C C 25 0 25 1 , I -chrM 9336 A A 12 0 25 1 , - -chrM 9337 C C 25 0 25 1 , < -chrM 9338 C C 25 0 25 1 , ? -chrM 9339 A A 25 0 25 1 , < -chrM 9340 C C 25 0 25 1 , I -chrM 9341 T T 25 0 25 1 , I -chrM 9342 T T 19 0 25 1 , 4 -chrM 9343 C C 25 0 25 1 , I -chrM 9344 G G 7 0 25 1 , ( -chrM 9345 G G 25 0 25 1 , I -chrM 9346 A A 16 0 25 1 , 1 -chrM 9347 T T 25 0 25 1 , I -chrM 9348 T T 25 0 25 1 , I -chrM 9349 C C 25 0 25 1 , I -chrM 9350 G G 33 0 25 2 ,^:. II +chrM 8943 C C 33 0 25 2 ,$, >I +chrM 8944 C C 30 0 25 1 , I +chrM 8945 T T 30 0 25 1 , I +chrM 8946 T T 30 0 25 1 , I +chrM 8947 T T 30 0 25 1 , I +chrM 8948 T T 30 0 25 1 , I +chrM 8949 A A 30 0 25 1 , I +chrM 8950 C C 30 0 25 1 , I +chrM 8951 C C 30 0 25 1 , I +chrM 8952 A A 30 0 25 1 , I +chrM 8953 C C 30 0 25 1 , I +chrM 8954 T T 30 0 25 1 , I +chrM 8955 C C 30 0 25 1 , I +chrM 8956 A N 0 0 0 1 n " +chrM 8957 A N 0 0 0 1 n " +chrM 8958 G G 30 0 25 1 , I +chrM 8959 C C 30 0 25 1 , I +chrM 8960 C C 30 0 25 1 , I +chrM 8961 T T 30 0 25 1 , I +chrM 8962 A A 30 0 25 1 , I +chrM 8963 G G 30 0 25 1 , I +chrM 8964 C C 30 0 25 1 ,$ > +chrM 9111 G G 30 0 25 1 ^:. E +chrM 9112 T T 30 0 25 1 . I +chrM 9113 A A 30 0 25 1 . I +chrM 9114 A A 30 0 25 1 . I +chrM 9115 A A 30 0 25 1 . I +chrM 9116 A A 30 0 25 1 . I +chrM 9117 A A 30 0 25 1 . I +chrM 9118 T N 0 0 0 1 N " +chrM 9119 A N 0 0 0 1 N " +chrM 9120 T T 30 0 25 1 . I +chrM 9121 G G 30 0 25 1 . I +chrM 9122 C C 30 0 25 1 . I +chrM 9123 T T 30 0 25 1 . I +chrM 9124 C C 30 0 25 1 . I +chrM 9125 C C 30 0 25 1 . I +chrM 9126 A A 30 0 25 1 . I +chrM 9127 A A 30 0 25 1 . I +chrM 9128 G G 30 0 25 1 . I +chrM 9129 G G 30 0 25 1 . I +chrM 9130 C C 30 0 25 1 . I +chrM 9131 C C 30 0 25 1 . I +chrM 9132 T T 30 0 25 1 . I +chrM 9133 A A 30 0 25 1 . I +chrM 9134 T T 30 0 25 1 . I +chrM 9135 T T 30 0 25 1 . I +chrM 9136 C C 30 0 25 1 . I +chrM 9137 A A 30 0 25 1 . I +chrM 9138 T T 30 0 25 1 . I +chrM 9139 C C 30 0 25 1 . I +chrM 9140 A A 30 0 25 1 . E +chrM 9141 C C 30 0 25 1 . I +chrM 9142 A A 30 0 25 1 . B +chrM 9143 A A 30 0 25 1 . 8 +chrM 9144 T T 30 0 25 1 . E +chrM 9145 T T 30 0 25 1 . B +chrM 9146 T T 30 0 25 1 .$ @ +chrM 9331 C N 0 0 0 1 ^:, & +chrM 9332 A N 0 0 0 1 , , +chrM 9333 G N 0 0 0 1 , * +chrM 9334 C C 30 0 25 1 , I +chrM 9335 C C 30 0 25 1 , I +chrM 9336 A N 0 0 0 1 , - +chrM 9337 C C 30 0 25 1 , < +chrM 9338 C C 30 0 25 1 , ? +chrM 9339 A A 30 0 25 1 , < +chrM 9340 C C 30 0 25 1 , I +chrM 9341 T T 30 0 25 1 , I +chrM 9342 T T 30 0 25 1 , 4 +chrM 9343 C C 30 0 25 1 , I +chrM 9344 G N 0 0 0 1 , ( +chrM 9345 G G 30 0 25 1 , I +chrM 9346 A A 30 0 25 1 , 1 +chrM 9347 T T 30 0 25 1 , I +chrM 9348 T T 30 0 25 1 , I +chrM 9349 C C 30 0 25 1 , I +chrM 9350 G G 33 0 25 2 ,^:. IE chrM 9351 A A 33 0 25 2 ,. II chrM 9352 A A 33 0 25 2 ,. DI chrM 9353 G G 33 0 25 2 ,. II chrM 9354 C C 33 0 25 2 ,. II chrM 9355 A A 33 0 25 2 ,. II chrM 9356 G G 33 0 25 2 ,. II -chrM 9357 C C 19 0 25 2 ,N I" -chrM 9358 C A 8 8 25 2 nN "" -chrM 9359 G G 19 0 25 2 n. "I +chrM 9357 C C 30 0 25 2 ,N I" +chrM 9358 C N 0 0 0 2 nN "" +chrM 9359 G G 30 0 25 2 n. "I chrM 9360 C C 33 0 25 2 ,. II chrM 9361 T T 33 0 25 2 ,. II chrM 9362 T T 33 0 25 2 ,. II chrM 9363 G G 33 0 25 2 ,. II chrM 9364 A A 33 0 25 2 ,. II chrM 9365 T T 33 0 25 2 ,. II -chrM 9366 A A 33 0 25 2 ,$. II -chrM 9367 C C 25 0 25 1 . I -chrM 9368 T T 25 0 25 1 . I -chrM 9369 G G 25 0 25 1 . I -chrM 9370 A A 25 0 25 1 . I -chrM 9371 C C 25 0 25 1 . I -chrM 9372 A A 25 0 25 1 . I -chrM 9373 C C 25 0 25 1 . I -chrM 9374 T T 25 0 25 1 . I -chrM 9375 T T 25 0 25 1 . I -chrM 9376 C C 25 0 25 1 . I -chrM 9377 G G 25 0 25 1 . I -chrM 9378 T T 25 0 25 1 . I -chrM 9379 C C 25 0 25 1 . I -chrM 9380 G G 25 0 25 1 . I -chrM 9381 A A 24 0 25 1 . 9 -chrM 9382 C C 25 0 25 1 . I -chrM 9383 G G 25 0 25 1 . I -chrM 9384 T T 25 0 25 1 . D -chrM 9385 A A 25 0 25 1 .$ F -chrM 9563 C C 25 0 25 1 ^:, I -chrM 9564 T T 10 0 25 1 , + -chrM 9565 G G 12 0 25 1 , - -chrM 9566 A A 25 0 25 1 , I -chrM 9567 C C 25 0 25 1 , I -chrM 9568 T T 25 0 25 1 , ? -chrM 9569 A A 25 0 25 1 , I -chrM 9570 C C 25 0 25 1 , D -chrM 9571 C C 25 0 25 1 , I -chrM 9572 A A 25 0 25 1 , I -chrM 9573 C C 25 0 25 1 , I -chrM 9574 A A 25 0 25 1 , I -chrM 9575 A A 25 0 25 1 , I -chrM 9576 C C 25 0 25 1 , I -chrM 9577 T T 25 0 25 1 , I -chrM 9578 A A 25 0 25 1 , I -chrM 9579 A A 25 0 25 1 , I -chrM 9580 A A 25 0 25 1 , I -chrM 9581 C C 25 0 25 1 , I -chrM 9582 A A 25 0 25 1 , I -chrM 9583 T T 25 0 25 1 , I -chrM 9584 C C 25 0 25 1 , I -chrM 9585 T T 25 0 25 1 , I -chrM 9586 A A 25 0 25 1 , I -chrM 9587 T T 25 0 25 1 , I -chrM 9588 G G 25 0 25 1 , I -chrM 9589 C C 25 0 25 1 , I -chrM 9590 A A 4 0 25 1 n " -chrM 9591 G A 4 4 25 1 n " -chrM 9592 A A 25 0 25 1 , I -chrM 9593 A A 25 0 25 1 , I -chrM 9594 A A 25 0 25 1 , I -chrM 9595 A A 25 0 25 1 , I -chrM 9596 A A 25 0 25 1 , I -chrM 9597 A A 25 0 25 1 , I -chrM 9598 C C 25 0 25 1 ,$ I -chrM 9689 A A 11 0 25 1 ^:, , -chrM 9690 T T 25 0 25 1 , C -chrM 9691 T T 25 0 25 1 , I -chrM 9692 C C 25 0 25 1 , I -chrM 9693 G G 25 0 25 1 , I -chrM 9694 A A 13 0 25 1 , . -chrM 9695 C C 25 0 25 1 , I -chrM 9696 T T 25 0 25 1 , I -chrM 9697 T T 15 0 25 1 , 0 -chrM 9698 A A 25 0 25 1 , I -chrM 9699 G G 25 0 25 1 , < -chrM 9700 A A 25 0 25 1 , I -chrM 9701 A A 25 0 25 1 , F -chrM 9702 A A 25 0 25 1 , I -chrM 9703 T T 25 0 25 1 , ; -chrM 9704 T T 25 0 25 1 , I -chrM 9705 G G 25 0 25 1 , I -chrM 9706 C C 25 0 25 1 , I -chrM 9707 C C 25 0 25 1 , I -chrM 9708 C C 25 0 25 1 , I -chrM 9709 T T 25 0 25 1 , D -chrM 9710 C C 25 0 25 1 , I -chrM 9711 C C 25 0 25 1 , I -chrM 9712 T T 25 0 25 1 , I -chrM 9713 A A 25 0 25 1 , I -chrM 9714 T T 25 0 25 1 , I -chrM 9715 T T 25 0 25 1 , I -chrM 9716 A A 4 0 25 1 n " -chrM 9717 C A 4 4 25 1 n " -chrM 9718 C C 25 0 25 1 , I -chrM 9719 C C 25 0 25 1 , I -chrM 9720 C C 25 0 25 1 , I -chrM 9721 T T 25 0 25 1 , I -chrM 9722 T T 5 0 25 1 , & -chrM 9723 C C 25 0 25 1 , I -chrM 9724 C C 25 0 25 1 ,$ I -chrM 9810 G G 25 0 25 1 ^:, A -chrM 9811 A A 25 0 25 1 , I -chrM 9812 A A 25 0 25 1 , I -chrM 9813 T T 25 0 25 1 , I -chrM 9814 G G 25 0 25 1 , I -chrM 9815 A A 25 0 25 1 , I -chrM 9816 A A 25 0 25 1 , I -chrM 9817 C C 25 0 25 1 , ? -chrM 9818 C C 17 0 25 1 , 2 -chrM 9819 C C 17 0 25 1 , 2 -chrM 9820 A A 25 0 25 1 , I -chrM 9821 A A 25 0 25 1 , I -chrM 9822 A A 25 0 25 1 , I -chrM 9823 A A 25 0 25 1 , I -chrM 9824 A A 25 0 25 1 , I -chrM 9825 G G 25 0 25 1 , I -chrM 9826 G G 25 0 25 1 , I -chrM 9827 A A 25 0 25 1 , I -chrM 9828 C C 25 0 25 1 , I -chrM 9829 T T 25 0 25 1 , I -chrM 9830 A A 25 0 25 1 , I -chrM 9831 G G 25 0 25 1 , I -chrM 9832 A A 25 0 25 1 , I -chrM 9833 A A 25 0 25 1 , I -chrM 9834 T T 25 0 25 1 , I -chrM 9835 G G 25 0 25 1 , I -chrM 9836 A A 25 0 25 1 , I -chrM 9837 A A 4 0 25 1 n " -chrM 9838 C A 4 4 25 1 n " -chrM 9839 T T 25 0 25 1 , I -chrM 9840 G G 25 0 25 1 , I -chrM 9841 A A 25 0 25 1 , I -chrM 9842 G G 25 0 25 1 , I -chrM 9843 T T 25 0 25 1 , I -chrM 9844 A A 25 0 25 1 , I -chrM 9845 T T 25 0 25 1 ,$ I -chrM 9916 T T 25 0 25 1 ^:. I -chrM 9917 G G 25 0 25 1 . I -chrM 9918 T T 25 0 25 1 . I -chrM 9919 C C 25 0 25 1 . I -chrM 9920 A A 25 0 25 1 . I -chrM 9921 C C 25 0 25 1 . I -chrM 9922 T T 25 0 25 1 . I -chrM 9923 A A 4 0 25 1 N " -chrM 9924 G A 4 4 25 1 N " -chrM 9925 T T 25 0 25 1 . I -chrM 9926 C C 25 0 25 1 . I -chrM 9927 C C 25 0 25 1 . I -chrM 9928 A A 25 0 25 1 . I -chrM 9929 T T 25 0 25 1 . I -chrM 9930 A A 25 0 25 1 . = -chrM 9931 T T 25 0 25 1 . I -chrM 9932 T T 25 0 25 1 . I -chrM 9933 A A 25 0 25 1 . I -chrM 9934 A A 24 0 25 1 . 9 -chrM 9935 T T 25 0 25 1 . I -chrM 9936 A A 25 0 25 1 . @ -chrM 9937 T T 25 0 25 1 . I -chrM 9938 C C 25 0 25 1 . I -chrM 9939 T T 25 0 25 1 . I -chrM 9940 T T 25 0 25 1 . I -chrM 9941 C C 25 0 25 1 . I -chrM 9942 C C 25 0 25 1 . I -chrM 9943 T T 25 0 25 1 . I -chrM 9944 A A 25 0 25 1 . B -chrM 9945 G G 25 0 25 1 . I -chrM 9946 C C 25 0 25 1 . I -chrM 9947 A A 25 0 25 1 . E -chrM 9948 T T 25 0 25 1 . I -chrM 9949 T T 25 0 25 1 . I -chrM 9950 C C 25 0 25 1 . I -chrM 9951 A A 25 0 25 1 .$ > -chrM 10002 C C 25 0 25 1 ^:, I -chrM 10003 T T 25 0 25 1 , : -chrM 10004 C C 17 0 25 1 , 2 -chrM 10005 C C 25 0 25 1 , I -chrM 10006 T T 25 0 25 1 , E -chrM 10007 A A 25 0 25 1 , I -chrM 10008 T T 25 0 25 1 , : -chrM 10009 G G 25 0 25 1 , I -chrM 10010 C C 25 0 25 1 , I -chrM 10011 C C 25 0 25 1 , D -chrM 10012 T T 25 0 25 1 , I -chrM 10013 A A 25 0 25 1 , I -chrM 10014 G G 25 0 25 1 , I -chrM 10015 A A 25 0 25 1 , I -chrM 10016 A A 25 0 25 1 , I -chrM 10017 G G 25 0 25 1 , I -chrM 10018 G G 19 0 25 1 , 4 -chrM 10019 A A 25 0 25 1 , I -chrM 10020 A A 25 0 25 1 , I -chrM 10021 T T 25 0 25 1 , I -chrM 10022 A A 25 0 25 1 , I -chrM 10023 A A 25 0 25 1 , I -chrM 10024 T T 25 0 25 1 , I -chrM 10025 A A 25 0 25 1 , I -chrM 10026 C C 25 0 25 1 , I -chrM 10027 T T 25 0 25 1 , I -chrM 10028 A A 25 0 25 1 , I -chrM 10029 T A 4 4 25 1 n " -chrM 10030 C A 4 4 25 1 n " -chrM 10031 A A 25 0 25 1 , I -chrM 10032 C C 25 0 25 1 , I -chrM 10033 T T 25 0 25 1 , I -chrM 10034 A A 25 0 25 1 , I -chrM 10035 T T 25 0 25 1 , I -chrM 10036 T T 25 0 25 1 , I -chrM 10037 C C 25 0 25 1 ,$ I -chrM 10391 G G 25 0 25 1 ^:. I -chrM 10392 C C 25 0 25 1 . I -chrM 10393 C C 25 0 25 1 . I -chrM 10394 C C 25 0 25 1 . I -chrM 10395 C C 25 0 25 1 . I -chrM 10396 A A 25 0 25 1 . I -chrM 10397 C C 25 0 25 1 . I -chrM 10398 T A 4 4 25 1 N " -chrM 10399 T A 4 4 25 1 N " -chrM 10400 C C 25 0 25 1 . I -chrM 10401 T T 25 0 25 1 . I -chrM 10402 G G 25 0 25 1 . I -chrM 10403 G G 25 0 25 1 . I -chrM 10404 T T 25 0 25 1 . I -chrM 10405 G G 25 0 25 1 . I -chrM 10406 T T 25 0 25 1 . I -chrM 10407 T T 25 0 25 1 . I -chrM 10408 G G 25 0 25 1 . I -chrM 10409 A A 25 0 25 1 . I -chrM 10410 C C 25 0 25 1 . I -chrM 10411 A A 25 0 25 1 . I -chrM 10412 A A 25 0 25 1 . I -chrM 10413 C C 25 0 25 1 . I -chrM 10414 A A 25 0 25 1 . = -chrM 10415 T T 25 0 25 1 . I -chrM 10416 G G 9 0 25 1 . * -chrM 10417 A A 20 0 25 1 . 5 -chrM 10418 C C 25 0 25 1 . I -chrM 10419 T T 25 0 25 1 . I -chrM 10420 A A 25 0 25 1 . < -chrM 10421 C C 25 0 25 1 . I -chrM 10422 T T 25 0 25 1 . I -chrM 10423 G G 6 0 25 1 . ' -chrM 10424 C C 25 0 25 1 . I -chrM 10425 C C 25 0 25 1 . I -chrM 10426 A A 7 0 25 1 .$ ( -chrM 10597 T T 25 0 25 1 ^:, H -chrM 10598 A A 25 0 25 1 , I -chrM 10599 T T 25 0 25 1 , < -chrM 10600 C C 25 0 25 1 , I -chrM 10601 A A 25 0 25 1 , I -chrM 10602 T T 25 0 25 1 , ; -chrM 10603 C C 25 0 25 1 , I -chrM 10604 A A 25 0 25 1 , I -chrM 10605 C C 25 0 25 1 , I -chrM 10606 C C 25 0 25 1 , I -chrM 10607 C C 25 0 25 1 , I -chrM 10608 G G 25 0 25 1 , I -chrM 10609 C C 25 0 25 1 , I -chrM 10610 T T 25 0 25 1 , I -chrM 10611 G G 25 0 25 1 , I -chrM 10612 A A 25 0 25 1 , I -chrM 10613 G G 25 0 25 1 , I -chrM 10614 G G 25 0 25 1 , I -chrM 10615 C C 25 0 25 1 , I -chrM 10616 A A 25 0 25 1 , I -chrM 10617 A A 33 0 25 2 ,^:, II +chrM 9366 A A 33 0 25 2 ,$. EI +chrM 9367 C C 30 0 25 1 . I +chrM 9368 T T 30 0 25 1 . I +chrM 9369 G G 30 0 25 1 . I +chrM 9370 A A 30 0 25 1 . I +chrM 9371 C C 30 0 25 1 . I +chrM 9372 A A 30 0 25 1 . I +chrM 9373 C C 30 0 25 1 . I +chrM 9374 T T 30 0 25 1 . I +chrM 9375 T T 30 0 25 1 . I +chrM 9376 C C 30 0 25 1 . I +chrM 9377 G G 30 0 25 1 . I +chrM 9378 T T 30 0 25 1 . I +chrM 9379 C C 30 0 25 1 . I +chrM 9380 G G 30 0 25 1 . I +chrM 9381 A A 30 0 25 1 . 9 +chrM 9382 C C 30 0 25 1 . I +chrM 9383 G G 30 0 25 1 . I +chrM 9384 T T 30 0 25 1 . D +chrM 9385 A A 30 0 25 1 .$ E +chrM 9563 C C 30 0 25 1 ^:, E +chrM 9564 T N 0 0 0 1 , + +chrM 9565 G N 0 0 0 1 , - +chrM 9566 A A 30 0 25 1 , I +chrM 9567 C C 30 0 25 1 , I +chrM 9568 T T 30 0 25 1 , ? +chrM 9569 A A 30 0 25 1 , I +chrM 9570 C C 30 0 25 1 , D +chrM 9571 C C 30 0 25 1 , I +chrM 9572 A A 30 0 25 1 , I +chrM 9573 C C 30 0 25 1 , I +chrM 9574 A A 30 0 25 1 , I +chrM 9575 A A 30 0 25 1 , I +chrM 9576 C C 30 0 25 1 , I +chrM 9577 T T 30 0 25 1 , I +chrM 9578 A A 30 0 25 1 , I +chrM 9579 A A 30 0 25 1 , I +chrM 9580 A A 30 0 25 1 , I +chrM 9581 C C 30 0 25 1 , I +chrM 9582 A A 30 0 25 1 , I +chrM 9583 T T 30 0 25 1 , I +chrM 9584 C C 30 0 25 1 , I +chrM 9585 T T 30 0 25 1 , I +chrM 9586 A A 30 0 25 1 , I +chrM 9587 T T 30 0 25 1 , I +chrM 9588 G G 30 0 25 1 , I +chrM 9589 C C 30 0 25 1 , I +chrM 9590 A N 0 0 0 1 n " +chrM 9591 G N 0 0 0 1 n " +chrM 9592 A A 30 0 25 1 , I +chrM 9593 A A 30 0 25 1 , I +chrM 9594 A A 30 0 25 1 , I +chrM 9595 A A 30 0 25 1 , I +chrM 9596 A A 30 0 25 1 , I +chrM 9597 A A 30 0 25 1 , I +chrM 9598 C C 30 0 25 1 ,$ > +chrM 9689 A N 0 0 0 1 ^:, , +chrM 9690 T T 30 0 25 1 , C +chrM 9691 T T 30 0 25 1 , I +chrM 9692 C C 30 0 25 1 , I +chrM 9693 G G 30 0 25 1 , I +chrM 9694 A A 30 0 25 1 , . +chrM 9695 C C 30 0 25 1 , I +chrM 9696 T T 30 0 25 1 , I +chrM 9697 T T 30 0 25 1 , 0 +chrM 9698 A A 30 0 25 1 , I +chrM 9699 G G 30 0 25 1 , < +chrM 9700 A A 30 0 25 1 , I +chrM 9701 A A 30 0 25 1 , F +chrM 9702 A A 30 0 25 1 , I +chrM 9703 T T 30 0 25 1 , ; +chrM 9704 T T 30 0 25 1 , I +chrM 9705 G G 30 0 25 1 , I +chrM 9706 C C 30 0 25 1 , I +chrM 9707 C C 30 0 25 1 , I +chrM 9708 C C 30 0 25 1 , I +chrM 9709 T T 30 0 25 1 , D +chrM 9710 C C 30 0 25 1 , I +chrM 9711 C C 30 0 25 1 , I +chrM 9712 T T 30 0 25 1 , I +chrM 9713 A A 30 0 25 1 , I +chrM 9714 T T 30 0 25 1 , I +chrM 9715 T T 30 0 25 1 , I +chrM 9716 A N 0 0 0 1 n " +chrM 9717 C N 0 0 0 1 n " +chrM 9718 C C 30 0 25 1 , I +chrM 9719 C C 30 0 25 1 , I +chrM 9720 C C 30 0 25 1 , I +chrM 9721 T T 30 0 25 1 , I +chrM 9722 T N 0 0 0 1 , & +chrM 9723 C C 30 0 25 1 , E +chrM 9724 C C 30 0 25 1 ,$ B +chrM 9810 G G 30 0 25 1 ^:, A +chrM 9811 A A 30 0 25 1 , I +chrM 9812 A A 30 0 25 1 , I +chrM 9813 T T 30 0 25 1 , I +chrM 9814 G G 30 0 25 1 , I +chrM 9815 A A 30 0 25 1 , I +chrM 9816 A A 30 0 25 1 , I +chrM 9817 C C 30 0 25 1 , ? +chrM 9818 C C 30 0 25 1 , 2 +chrM 9819 C C 30 0 25 1 , 2 +chrM 9820 A A 30 0 25 1 , I +chrM 9821 A A 30 0 25 1 , I +chrM 9822 A A 30 0 25 1 , I +chrM 9823 A A 30 0 25 1 , I +chrM 9824 A A 30 0 25 1 , I +chrM 9825 G G 30 0 25 1 , I +chrM 9826 G G 30 0 25 1 , I +chrM 9827 A A 30 0 25 1 , I +chrM 9828 C C 30 0 25 1 , I +chrM 9829 T T 30 0 25 1 , I +chrM 9830 A A 30 0 25 1 , I +chrM 9831 G G 30 0 25 1 , I +chrM 9832 A A 30 0 25 1 , I +chrM 9833 A A 30 0 25 1 , I +chrM 9834 T T 30 0 25 1 , I +chrM 9835 G G 30 0 25 1 , I +chrM 9836 A A 30 0 25 1 , I +chrM 9837 A N 0 0 0 1 n " +chrM 9838 C N 0 0 0 1 n " +chrM 9839 T T 30 0 25 1 , I +chrM 9840 G G 30 0 25 1 , I +chrM 9841 A A 30 0 25 1 , I +chrM 9842 G G 30 0 25 1 , I +chrM 9843 T T 30 0 25 1 , I +chrM 9844 A A 30 0 25 1 , I +chrM 9845 T T 30 0 25 1 ,$ E +chrM 9916 T T 30 0 25 1 ^:. E +chrM 9917 G G 30 0 25 1 . I +chrM 9918 T T 30 0 25 1 . I +chrM 9919 C C 30 0 25 1 . I +chrM 9920 A A 30 0 25 1 . I +chrM 9921 C C 30 0 25 1 . I +chrM 9922 T T 30 0 25 1 . I +chrM 9923 A N 0 0 0 1 N " +chrM 9924 G N 0 0 0 1 N " +chrM 9925 T T 30 0 25 1 . I +chrM 9926 C C 30 0 25 1 . I +chrM 9927 C C 30 0 25 1 . I +chrM 9928 A A 30 0 25 1 . I +chrM 9929 T T 30 0 25 1 . I +chrM 9930 A A 30 0 25 1 . = +chrM 9931 T T 30 0 25 1 . I +chrM 9932 T T 30 0 25 1 . I +chrM 9933 A A 30 0 25 1 . I +chrM 9934 A A 30 0 25 1 . 9 +chrM 9935 T T 30 0 25 1 . I +chrM 9936 A A 30 0 25 1 . @ +chrM 9937 T T 30 0 25 1 . I +chrM 9938 C C 30 0 25 1 . I +chrM 9939 T T 30 0 25 1 . I +chrM 9940 T T 30 0 25 1 . I +chrM 9941 C C 30 0 25 1 . I +chrM 9942 C C 30 0 25 1 . I +chrM 9943 T T 30 0 25 1 . I +chrM 9944 A A 30 0 25 1 . B +chrM 9945 G G 30 0 25 1 . I +chrM 9946 C C 30 0 25 1 . I +chrM 9947 A A 30 0 25 1 . E +chrM 9948 T T 30 0 25 1 . I +chrM 9949 T T 30 0 25 1 . I +chrM 9950 C C 30 0 25 1 . I +chrM 9951 A A 30 0 25 1 .$ > +chrM 10002 C C 30 0 25 1 ^:, E +chrM 10003 T T 30 0 25 1 , : +chrM 10004 C C 30 0 25 1 , 2 +chrM 10005 C C 30 0 25 1 , I +chrM 10006 T T 30 0 25 1 , E +chrM 10007 A A 30 0 25 1 , I +chrM 10008 T T 30 0 25 1 , : +chrM 10009 G G 30 0 25 1 , I +chrM 10010 C C 30 0 25 1 , I +chrM 10011 C C 30 0 25 1 , D +chrM 10012 T T 30 0 25 1 , I +chrM 10013 A A 30 0 25 1 , I +chrM 10014 G G 30 0 25 1 , I +chrM 10015 A A 30 0 25 1 , I +chrM 10016 A A 30 0 25 1 , I +chrM 10017 G G 30 0 25 1 , I +chrM 10018 G G 30 0 25 1 , 4 +chrM 10019 A A 30 0 25 1 , I +chrM 10020 A A 30 0 25 1 , I +chrM 10021 T T 30 0 25 1 , I +chrM 10022 A A 30 0 25 1 , I +chrM 10023 A A 30 0 25 1 , I +chrM 10024 T T 30 0 25 1 , I +chrM 10025 A A 30 0 25 1 , I +chrM 10026 C C 30 0 25 1 , I +chrM 10027 T T 30 0 25 1 , I +chrM 10028 A A 30 0 25 1 , I +chrM 10029 T N 0 0 0 1 n " +chrM 10030 C N 0 0 0 1 n " +chrM 10031 A A 30 0 25 1 , I +chrM 10032 C C 30 0 25 1 , I +chrM 10033 T T 30 0 25 1 , I +chrM 10034 A A 30 0 25 1 , I +chrM 10035 T T 30 0 25 1 , I +chrM 10036 T T 30 0 25 1 , I +chrM 10037 C C 30 0 25 1 ,$ E +chrM 10391 G G 30 0 25 1 ^:. E +chrM 10392 C C 30 0 25 1 . I +chrM 10393 C C 30 0 25 1 . I +chrM 10394 C C 30 0 25 1 . I +chrM 10395 C C 30 0 25 1 . I +chrM 10396 A A 30 0 25 1 . I +chrM 10397 C C 30 0 25 1 . I +chrM 10398 T N 0 0 0 1 N " +chrM 10399 T N 0 0 0 1 N " +chrM 10400 C C 30 0 25 1 . I +chrM 10401 T T 30 0 25 1 . I +chrM 10402 G G 30 0 25 1 . I +chrM 10403 G G 30 0 25 1 . I +chrM 10404 T T 30 0 25 1 . I +chrM 10405 G G 30 0 25 1 . I +chrM 10406 T T 30 0 25 1 . I +chrM 10407 T T 30 0 25 1 . I +chrM 10408 G G 30 0 25 1 . I +chrM 10409 A A 30 0 25 1 . I +chrM 10410 C C 30 0 25 1 . I +chrM 10411 A A 30 0 25 1 . I +chrM 10412 A A 30 0 25 1 . I +chrM 10413 C C 30 0 25 1 . I +chrM 10414 A A 30 0 25 1 . = +chrM 10415 T T 30 0 25 1 . I +chrM 10416 G N 0 0 0 1 . * +chrM 10417 A A 30 0 25 1 . 5 +chrM 10418 C C 30 0 25 1 . I +chrM 10419 T T 30 0 25 1 . I +chrM 10420 A A 30 0 25 1 . < +chrM 10421 C C 30 0 25 1 . I +chrM 10422 T T 30 0 25 1 . I +chrM 10423 G N 0 0 0 1 . ' +chrM 10424 C C 30 0 25 1 . I +chrM 10425 C C 30 0 25 1 . I +chrM 10426 A N 0 0 0 1 .$ ( +chrM 10597 T T 30 0 25 1 ^:, E +chrM 10598 A A 30 0 25 1 , I +chrM 10599 T T 30 0 25 1 , < +chrM 10600 C C 30 0 25 1 , I +chrM 10601 A A 30 0 25 1 , I +chrM 10602 T T 30 0 25 1 , ; +chrM 10603 C C 30 0 25 1 , I +chrM 10604 A A 30 0 25 1 , I +chrM 10605 C C 30 0 25 1 , I +chrM 10606 C C 30 0 25 1 , I +chrM 10607 C C 30 0 25 1 , I +chrM 10608 G G 30 0 25 1 , I +chrM 10609 C C 30 0 25 1 , I +chrM 10610 T T 30 0 25 1 , I +chrM 10611 G G 30 0 25 1 , I +chrM 10612 A A 30 0 25 1 , I +chrM 10613 G G 30 0 25 1 , I +chrM 10614 G G 30 0 25 1 , I +chrM 10615 C C 30 0 25 1 , I +chrM 10616 A A 30 0 25 1 , I +chrM 10617 A A 33 0 25 2 ,^:, IE chrM 10618 C C 33 0 25 2 ,, II chrM 10619 C C 33 0 25 2 ,, II chrM 10620 A A 33 0 25 2 ,, II chrM 10621 A A 33 0 25 2 ,, II chrM 10622 A A 33 0 25 2 ,, II chrM 10623 C C 33 0 25 2 ,, II -chrM 10624 A A 28 0 25 2 n, "I -chrM 10625 G G 19 0 25 2 n, "I +chrM 10624 A A 30 0 25 2 n, "I +chrM 10625 G G 30 0 25 2 n, "I chrM 10626 A A 33 0 25 2 ,, II chrM 10627 A A 33 0 25 2 ,, II chrM 10628 C C 33 0 25 2 ,, II chrM 10629 G G 33 0 25 2 ,, II chrM 10630 C C 33 0 25 2 ,, II chrM 10631 C C 33 0 25 2 ,, II -chrM 10632 T T 33 0 25 2 ,$, II -chrM 10633 G G 25 0 25 1 , I -chrM 10634 A A 25 0 25 1 , I -chrM 10635 A A 25 0 25 1 , I -chrM 10636 C C 25 0 25 1 , I -chrM 10637 G G 25 0 25 1 , I -chrM 10638 C C 25 0 25 1 , I -chrM 10639 A A 25 0 25 1 , I -chrM 10640 G G 25 0 25 1 , I -chrM 10641 G G 25 0 25 1 , I -chrM 10642 C C 25 0 25 1 , I -chrM 10643 C C 25 0 25 1 , I -chrM 10644 T A 4 4 25 1 n " -chrM 10645 C A 4 4 25 1 n " -chrM 10646 T T 25 0 25 1 , I -chrM 10647 A A 25 0 25 1 , I -chrM 10648 C C 25 0 25 1 , I -chrM 10649 T T 25 0 25 1 , I -chrM 10650 T T 25 0 25 1 , I -chrM 10651 C C 25 0 25 1 , I -chrM 10652 C C 25 0 25 1 ,$ I -chrM 10669 A A 25 0 25 1 ^:, I -chrM 10670 G G 25 0 25 1 , I -chrM 10671 G G 25 0 25 1 , I -chrM 10672 T T 25 0 25 1 , I -chrM 10673 T T 25 0 25 1 , < -chrM 10674 C C 25 0 25 1 , I -chrM 10675 C C 25 0 25 1 , I -chrM 10676 C C 25 0 25 1 , I -chrM 10677 T T 25 0 25 1 , C -chrM 10678 C C 25 0 25 1 , I -chrM 10679 C C 25 0 25 1 , I -chrM 10680 C C 25 0 25 1 , I -chrM 10681 A A 25 0 25 1 , I -chrM 10682 C C 25 0 25 1 , I -chrM 10683 T T 25 0 25 1 , I -chrM 10684 C C 25 0 25 1 , I -chrM 10685 T T 25 0 25 1 , F -chrM 10686 T T 25 0 25 1 , I -chrM 10687 A A 25 0 25 1 , I -chrM 10688 G G 25 0 25 1 , I -chrM 10689 T T 25 0 25 1 , I -chrM 10690 T T 25 0 25 1 , I -chrM 10691 G G 25 0 25 1 , I -chrM 10692 C C 25 0 25 1 , I -chrM 10693 A A 25 0 25 1 , I -chrM 10694 C C 25 0 25 1 , I -chrM 10695 T T 25 0 25 1 , I -chrM 10696 A A 4 0 25 1 n " -chrM 10697 A A 4 0 25 1 n " -chrM 10698 T T 25 0 25 1 , I -chrM 10699 C C 25 0 25 1 , I -chrM 10700 T T 25 0 25 1 , I -chrM 10701 C C 25 0 25 1 , I -chrM 10702 T T 25 0 25 1 , I -chrM 10703 A A 25 0 25 1 , I -chrM 10704 T T 25 0 25 1 ,$ I -chrM 10731 T T 25 0 25 1 ^:. I -chrM 10732 C C 25 0 25 1 . I -chrM 10733 C C 25 0 25 1 . I -chrM 10734 T T 25 0 25 1 . I -chrM 10735 A A 25 0 25 1 . I -chrM 10736 T T 25 0 25 1 . I -chrM 10737 T T 25 0 25 1 . I -chrM 10738 A A 4 0 25 1 N " -chrM 10739 A A 4 0 25 1 N " -chrM 10740 T T 25 0 25 1 . I -chrM 10741 T T 25 0 25 1 . I -chrM 10742 C C 25 0 25 1 . I -chrM 10743 A A 25 0 25 1 . I -chrM 10744 A A 25 0 25 1 . I -chrM 10745 T T 25 0 25 1 . I -chrM 10746 A A 25 0 25 1 . I -chrM 10747 C C 25 0 25 1 . I -chrM 10748 T T 25 0 25 1 . I -chrM 10749 G G 25 0 25 1 . I -chrM 10750 A A 25 0 25 1 . I -chrM 10751 A A 25 0 25 1 . I -chrM 10752 A A 25 0 25 1 . I -chrM 10753 C C 25 0 25 1 . I -chrM 10754 C C 25 0 25 1 . I -chrM 10755 A A 25 0 25 1 . I -chrM 10756 A A 25 0 25 1 . F -chrM 10757 G G 25 0 25 1 . I -chrM 10758 C C 25 0 25 1 . I -chrM 10759 A A 25 0 25 1 . I -chrM 10760 C C 25 0 25 1 . I -chrM 10761 T T 25 0 25 1 . I -chrM 10762 A A 25 0 25 1 . @ -chrM 10763 C C 25 0 25 1 . I -chrM 10764 C C 25 0 25 1 . I -chrM 10765 C C 25 0 25 1 . I -chrM 10766 G G 25 0 25 1 .$ H -chrM 10784 T T 25 0 25 1 ^:, E -chrM 10785 T T 24 0 25 1 , 9 -chrM 10786 C C 25 0 25 1 , I -chrM 10787 C C 14 0 25 1 , / -chrM 10788 T T 25 0 25 1 , B -chrM 10789 A A 25 0 25 1 , I -chrM 10790 T T 25 0 25 1 , I -chrM 10791 G G 25 0 25 1 , I -chrM 10792 A A 25 0 25 1 , I -chrM 10793 C C 25 0 25 1 , C -chrM 10794 T T 25 0 25 1 , I -chrM 10795 A A 25 0 25 1 , I -chrM 10796 G G 25 0 25 1 , I -chrM 10797 C C 25 0 25 1 , I -chrM 10798 A A 25 0 25 1 , I -chrM 10799 T T 25 0 25 1 , F -chrM 10800 G G 25 0 25 1 , I -chrM 10801 T T 25 0 25 1 , I -chrM 10802 A A 25 0 25 1 , I -chrM 10803 T T 25 0 25 1 , I -chrM 10804 A A 25 0 25 1 , I -chrM 10805 A A 25 0 25 1 , I -chrM 10806 T T 25 0 25 1 , I -chrM 10807 A A 25 0 25 1 , I -chrM 10808 G G 25 0 25 1 , I -chrM 10809 C C 25 0 25 1 , I -chrM 10810 A A 25 0 25 1 , I -chrM 10811 T A 4 4 25 1 n " -chrM 10812 T A 4 4 25 1 n " -chrM 10813 C C 25 0 25 1 , I -chrM 10814 A A 25 0 25 1 , I -chrM 10815 T T 25 0 25 1 , I -chrM 10816 A A 25 0 25 1 , I -chrM 10817 G G 25 0 25 1 , I -chrM 10818 T T 25 0 25 1 , I -chrM 10819 C C 25 0 25 1 ,$ I -chrM 10864 T T 25 0 25 1 ^:, D -chrM 10865 G G 25 0 25 1 , B -chrM 10866 T T 25 0 25 1 , A -chrM 10867 A A 25 0 25 1 , I -chrM 10868 G G 25 0 25 1 , I -chrM 10869 A A 25 0 25 1 , I -chrM 10870 A A 25 0 25 1 , I -chrM 10871 G G 25 0 25 1 , I -chrM 10872 C C 25 0 25 1 , I -chrM 10873 C C 25 0 25 1 , I -chrM 10874 C C 25 0 25 1 , I -chrM 10875 C C 25 0 25 1 , I -chrM 10876 A A 25 0 25 1 , I -chrM 10877 A A 25 0 25 1 , I -chrM 10878 T T 25 0 25 1 , F -chrM 10879 T T 25 0 25 1 , I -chrM 10880 G G 25 0 25 1 , I -chrM 10881 C C 25 0 25 1 , I -chrM 10882 C C 25 0 25 1 , I -chrM 10883 G G 25 0 25 1 , I -chrM 10884 G G 25 0 25 1 , I -chrM 10885 A A 25 0 25 1 , I -chrM 10886 T T 25 0 25 1 , I -chrM 10887 C C 25 0 25 1 , I -chrM 10888 C C 25 0 25 1 , I -chrM 10889 A A 25 0 25 1 , I -chrM 10890 T T 25 0 25 1 , I -chrM 10891 A A 23 0 25 2 n^:, "5 -chrM 10892 G G 16 0 25 2 n, "7 -chrM 10893 T T 33 0 25 2 ,, I- +chrM 10632 T T 33 0 25 2 ,$, EI +chrM 10633 G G 30 0 25 1 , I +chrM 10634 A A 30 0 25 1 , I +chrM 10635 A A 30 0 25 1 , I +chrM 10636 C C 30 0 25 1 , I +chrM 10637 G G 30 0 25 1 , I +chrM 10638 C C 30 0 25 1 , I +chrM 10639 A A 30 0 25 1 , I +chrM 10640 G G 30 0 25 1 , I +chrM 10641 G G 30 0 25 1 , I +chrM 10642 C C 30 0 25 1 , I +chrM 10643 C C 30 0 25 1 , I +chrM 10644 T N 0 0 0 1 n " +chrM 10645 C N 0 0 0 1 n " +chrM 10646 T T 30 0 25 1 , I +chrM 10647 A A 30 0 25 1 , I +chrM 10648 C C 30 0 25 1 , I +chrM 10649 T T 30 0 25 1 , I +chrM 10650 T T 30 0 25 1 , I +chrM 10651 C C 30 0 25 1 , E +chrM 10652 C C 30 0 25 1 ,$ B +chrM 10669 A A 30 0 25 1 ^:, E +chrM 10670 G G 30 0 25 1 , I +chrM 10671 G G 30 0 25 1 , I +chrM 10672 T T 30 0 25 1 , I +chrM 10673 T T 30 0 25 1 , < +chrM 10674 C C 30 0 25 1 , I +chrM 10675 C C 30 0 25 1 , I +chrM 10676 C C 30 0 25 1 , I +chrM 10677 T T 30 0 25 1 , C +chrM 10678 C C 30 0 25 1 , I +chrM 10679 C C 30 0 25 1 , I +chrM 10680 C C 30 0 25 1 , I +chrM 10681 A A 30 0 25 1 , I +chrM 10682 C C 30 0 25 1 , I +chrM 10683 T T 30 0 25 1 , I +chrM 10684 C C 30 0 25 1 , I +chrM 10685 T T 30 0 25 1 , F +chrM 10686 T T 30 0 25 1 , I +chrM 10687 A A 30 0 25 1 , I +chrM 10688 G G 30 0 25 1 , I +chrM 10689 T T 30 0 25 1 , I +chrM 10690 T T 30 0 25 1 , I +chrM 10691 G G 30 0 25 1 , I +chrM 10692 C C 30 0 25 1 , I +chrM 10693 A A 30 0 25 1 , I +chrM 10694 C C 30 0 25 1 , I +chrM 10695 T T 30 0 25 1 , I +chrM 10696 A N 0 0 0 1 n " +chrM 10697 A N 0 0 0 1 n " +chrM 10698 T T 30 0 25 1 , I +chrM 10699 C C 30 0 25 1 , I +chrM 10700 T T 30 0 25 1 , I +chrM 10701 C C 30 0 25 1 , I +chrM 10702 T T 30 0 25 1 , I +chrM 10703 A A 30 0 25 1 , I +chrM 10704 T T 30 0 25 1 ,$ E +chrM 10731 T T 30 0 25 1 ^:. E +chrM 10732 C C 30 0 25 1 . I +chrM 10733 C C 30 0 25 1 . I +chrM 10734 T T 30 0 25 1 . I +chrM 10735 A A 30 0 25 1 . I +chrM 10736 T T 30 0 25 1 . I +chrM 10737 T T 30 0 25 1 . I +chrM 10738 A N 0 0 0 1 N " +chrM 10739 A N 0 0 0 1 N " +chrM 10740 T T 30 0 25 1 . I +chrM 10741 T T 30 0 25 1 . I +chrM 10742 C C 30 0 25 1 . I +chrM 10743 A A 30 0 25 1 . I +chrM 10744 A A 30 0 25 1 . I +chrM 10745 T T 30 0 25 1 . I +chrM 10746 A A 30 0 25 1 . I +chrM 10747 C C 30 0 25 1 . I +chrM 10748 T T 30 0 25 1 . I +chrM 10749 G G 30 0 25 1 . I +chrM 10750 A A 30 0 25 1 . I +chrM 10751 A A 30 0 25 1 . I +chrM 10752 A A 30 0 25 1 . I +chrM 10753 C C 30 0 25 1 . I +chrM 10754 C C 30 0 25 1 . I +chrM 10755 A A 30 0 25 1 . I +chrM 10756 A A 30 0 25 1 . F +chrM 10757 G G 30 0 25 1 . I +chrM 10758 C C 30 0 25 1 . I +chrM 10759 A A 30 0 25 1 . I +chrM 10760 C C 30 0 25 1 . I +chrM 10761 T T 30 0 25 1 . I +chrM 10762 A A 30 0 25 1 . @ +chrM 10763 C C 30 0 25 1 . I +chrM 10764 C C 30 0 25 1 . I +chrM 10765 C C 30 0 25 1 . I +chrM 10766 G G 30 0 25 1 .$ E +chrM 10784 T T 30 0 25 1 ^:, = +chrM 10785 T T 30 0 25 1 , 9 +chrM 10786 C C 30 0 25 1 , I +chrM 10787 C C 30 0 25 1 , / +chrM 10788 T T 30 0 25 1 , B +chrM 10789 A A 30 0 25 1 , I +chrM 10790 T T 30 0 25 1 , I +chrM 10791 G G 30 0 25 1 , I +chrM 10792 A A 30 0 25 1 , I +chrM 10793 C C 30 0 25 1 , C +chrM 10794 T T 30 0 25 1 , I +chrM 10795 A A 30 0 25 1 , I +chrM 10796 G G 30 0 25 1 , I +chrM 10797 C C 30 0 25 1 , I +chrM 10798 A A 30 0 25 1 , I +chrM 10799 T T 30 0 25 1 , F +chrM 10800 G G 30 0 25 1 , I +chrM 10801 T T 30 0 25 1 , I +chrM 10802 A A 30 0 25 1 , I +chrM 10803 T T 30 0 25 1 , I +chrM 10804 A A 30 0 25 1 , I +chrM 10805 A A 30 0 25 1 , I +chrM 10806 T T 30 0 25 1 , I +chrM 10807 A A 30 0 25 1 , I +chrM 10808 G G 30 0 25 1 , I +chrM 10809 C C 30 0 25 1 , I +chrM 10810 A A 30 0 25 1 , I +chrM 10811 T N 0 0 0 1 n " +chrM 10812 T N 0 0 0 1 n " +chrM 10813 C C 30 0 25 1 , I +chrM 10814 A A 30 0 25 1 , I +chrM 10815 T T 30 0 25 1 , I +chrM 10816 A A 30 0 25 1 , I +chrM 10817 G G 30 0 25 1 , I +chrM 10818 T T 30 0 25 1 , I +chrM 10819 C C 30 0 25 1 ,$ E +chrM 10864 T T 30 0 25 1 ^:, D +chrM 10865 G G 30 0 25 1 , B +chrM 10866 T T 30 0 25 1 , A +chrM 10867 A A 30 0 25 1 , I +chrM 10868 G G 30 0 25 1 , I +chrM 10869 A A 30 0 25 1 , I +chrM 10870 A A 30 0 25 1 , I +chrM 10871 G G 30 0 25 1 , I +chrM 10872 C C 30 0 25 1 , I +chrM 10873 C C 30 0 25 1 , I +chrM 10874 C C 30 0 25 1 , I +chrM 10875 C C 30 0 25 1 , I +chrM 10876 A A 30 0 25 1 , I +chrM 10877 A A 30 0 25 1 , I +chrM 10878 T T 30 0 25 1 , F +chrM 10879 T T 30 0 25 1 , I +chrM 10880 G G 30 0 25 1 , I +chrM 10881 C C 30 0 25 1 , I +chrM 10882 C C 30 0 25 1 , I +chrM 10883 G G 30 0 25 1 , I +chrM 10884 G G 30 0 25 1 , I +chrM 10885 A A 30 0 25 1 , I +chrM 10886 T T 30 0 25 1 , I +chrM 10887 C C 30 0 25 1 , I +chrM 10888 C C 30 0 25 1 , I +chrM 10889 A A 30 0 25 1 , I +chrM 10890 T T 30 0 25 1 , I +chrM 10891 A A 30 0 25 2 n^:, "5 +chrM 10892 G G 30 0 25 2 n, "7 +chrM 10893 T T 30 0 25 2 ,, I- chrM 10894 G G 33 0 25 2 ,, IC chrM 10895 C C 33 0 25 2 ,, I5 -chrM 10896 T T 33 0 25 2 ,, I, +chrM 10896 T T 30 0 25 2 ,, I, chrM 10897 A A 33 0 25 2 ,, II chrM 10898 G G 33 0 25 2 ,, I5 -chrM 10899 C C 33 0 25 2 ,$, II -chrM 10900 A A 25 0 25 1 , I -chrM 10901 G G 25 0 25 1 , I +chrM 10899 C C 33 0 25 2 ,$, DI +chrM 10900 A A 30 0 25 1 , I +chrM 10901 G G 30 0 25 1 , I chrM 10902 C C 30 0 25 2 ,^:, I' chrM 10903 C C 33 0 25 2 ,, IA chrM 10904 A A 33 0 25 2 ,, II @@ -2287,579 +2287,579 @@ chrM 10914 A A 33 0 25 2 ,, II chrM 10915 A A 33 0 25 2 ,, I8 chrM 10916 C C 33 0 25 2 ,, I6 chrM 10917 T T 33 0 25 2 ,, I. -chrM 10918 A A 28 0 25 2 n, "I -chrM 10919 G G 19 0 25 2 n, "I +chrM 10918 A A 30 0 25 2 n, "I +chrM 10919 G G 30 0 25 2 n, "I chrM 10920 G G 33 0 25 2 ,, II chrM 10921 A A 33 0 25 2 ,, II chrM 10922 G G 33 0 25 2 ,, II chrM 10923 G G 33 0 25 2 ,, II chrM 10924 C C 33 0 25 2 ,, II chrM 10925 T T 33 0 25 2 ,, II -chrM 10926 A A 33 0 25 2 ,$, II -chrM 10927 C C 25 0 25 1 , I -chrM 10928 G G 25 0 25 1 , I -chrM 10929 G A 4 4 25 1 n " -chrM 10930 A A 4 0 25 1 n " -chrM 10931 A A 25 0 25 1 , I -chrM 10932 T T 25 0 25 1 , I -chrM 10933 A A 25 0 25 1 , I -chrM 10934 C C 25 0 25 1 , I -chrM 10935 T T 25 0 25 1 , I -chrM 10936 A A 25 0 25 1 , I -chrM 10937 C C 22 0 25 1 ,$ 7 -chrM 10991 A A 25 0 25 1 ^:. I -chrM 10992 T T 25 0 25 1 . I -chrM 10993 A A 25 0 25 1 . I -chrM 10994 C C 25 0 25 1 . I -chrM 10995 T T 25 0 25 1 . I -chrM 10996 A A 25 0 25 1 . I -chrM 10997 T T 25 0 25 1 . I -chrM 10998 C A 4 4 25 1 N " -chrM 10999 C A 4 4 25 1 N " -chrM 11000 C C 25 0 25 1 . I -chrM 11001 T T 25 0 25 1 . I -chrM 11002 G G 25 0 25 1 . I -chrM 11003 T T 25 0 25 1 . I -chrM 11004 G G 25 0 25 1 . I -chrM 11005 A A 17 0 25 1 . 2 -chrM 11006 G G 25 0 25 1 . I -chrM 11007 G G 25 0 25 1 . I -chrM 11008 A A 25 0 25 1 . I -chrM 11009 A A 25 0 25 1 . I -chrM 11010 T T 25 0 25 1 . I -chrM 11011 A A 25 0 25 1 . I -chrM 11012 A A 25 0 25 1 . I -chrM 11013 T T 25 0 25 1 . I -chrM 11014 C C 25 0 25 1 . I -chrM 11015 A A 25 0 25 1 . I -chrM 11016 T T 25 0 25 1 . I -chrM 11017 A A 25 0 25 1 . F -chrM 11018 A A 25 0 25 1 . I -chrM 11019 C C 25 0 25 1 . I -chrM 11020 T T 25 0 25 1 . I -chrM 11021 A A 25 0 25 1 . : -chrM 11022 G G 25 0 25 1 . I -chrM 11023 T T 25 0 25 1 . I -chrM 11024 T T 25 0 25 1 . I -chrM 11025 C C 25 0 25 1 . I -chrM 11026 C C 25 0 25 1 .$ I -chrM 11036 C C 25 0 25 1 ^:, I -chrM 11037 G G 25 0 25 1 , I -chrM 11038 A A 25 0 25 1 , I -chrM 11039 C C 25 0 25 1 , I -chrM 11040 A A 25 0 25 1 , I -chrM 11041 A A 25 0 25 1 , I -chrM 11042 A A 25 0 25 1 , I -chrM 11043 C C 25 0 25 1 , I -chrM 11044 C C 25 0 25 1 , I -chrM 11045 G G 25 0 25 1 , I -chrM 11046 A A 25 0 25 1 , I -chrM 11047 T T 25 0 25 1 , I -chrM 11048 C C 25 0 25 1 , I -chrM 11049 T T 25 0 25 1 , I -chrM 11050 A A 25 0 25 1 , I -chrM 11051 A A 25 0 25 1 , I -chrM 11052 A A 25 0 25 1 , I -chrM 11053 A A 25 0 25 1 , I -chrM 11054 T T 25 0 25 1 , I -chrM 11055 C C 25 0 25 1 , I -chrM 11056 A A 25 0 25 1 , I -chrM 11057 C C 25 0 25 1 , I -chrM 11058 T T 25 0 25 1 , I -chrM 11059 T T 25 0 25 1 , I -chrM 11060 A A 25 0 25 1 , I -chrM 11061 T T 25 0 25 1 , I -chrM 11062 T T 25 0 25 1 , I -chrM 11063 G A 4 4 25 1 n " -chrM 11064 C A 4 4 25 1 n " -chrM 11065 A A 25 0 25 1 , I -chrM 11066 T T 25 0 25 1 , I -chrM 11067 A A 25 0 25 1 , I -chrM 11068 C C 25 0 25 1 , I -chrM 11069 T T 25 0 25 1 , I -chrM 11070 C C 25 0 25 1 , I -chrM 11071 C C 25 0 25 1 ,$ I -chrM 11086 A A 25 0 25 1 ^:, I -chrM 11087 G G 16 0 25 1 , 1 -chrM 11088 C C 6 0 25 1 , ' -chrM 11089 C C 25 0 25 1 , = -chrM 11090 C C 25 0 25 1 , D -chrM 11091 T T 15 0 25 1 , 0 -chrM 11092 A A 25 0 25 1 , I -chrM 11093 G G 25 0 25 1 , @ -chrM 11094 T T 19 0 25 1 , 4 -chrM 11095 A A 25 0 25 1 , I -chrM 11096 A A 25 0 25 1 , I -chrM 11097 T T 25 0 25 1 , A -chrM 11098 C C 25 0 25 1 , I -chrM 11099 G G 25 0 25 1 , I -chrM 11100 T T 25 0 25 1 , D -chrM 11101 A A 25 0 25 1 , I -chrM 11102 G G 25 0 25 1 , I -chrM 11103 C C 25 0 25 1 , I -chrM 11104 C C 25 0 25 1 , I -chrM 11105 G G 25 0 25 1 , I -chrM 11106 T T 25 0 25 1 , I -chrM 11107 C C 25 0 25 1 , I -chrM 11108 C C 25 0 25 1 , I -chrM 11109 T T 25 0 25 1 , I -chrM 11110 C C 25 0 25 1 , I -chrM 11111 A A 25 0 25 1 , I -chrM 11112 T T 25 0 25 1 , I -chrM 11113 C A 4 4 25 1 n " -chrM 11114 C A 4 4 25 1 n " -chrM 11115 A A 25 0 25 1 , I -chrM 11116 A A 25 0 25 1 , I -chrM 11117 A A 25 0 25 1 , I -chrM 11118 C C 25 0 25 1 , I -chrM 11119 A A 25 0 25 1 , I -chrM 11120 C C 25 0 25 1 , I -chrM 11121 C C 25 0 25 1 ,$ I -chrM 11375 A A 25 0 25 1 ^:. I -chrM 11376 T T 25 0 25 1 . I -chrM 11377 T T 25 0 25 1 . I -chrM 11378 A A 25 0 25 1 . I -chrM 11379 C C 25 0 25 1 . I -chrM 11380 C C 25 0 25 1 . I -chrM 11381 A A 25 0 25 1 . I -chrM 11382 T A 4 4 25 1 N " -chrM 11383 T A 4 4 25 1 N " -chrM 11384 A A 25 0 25 1 . I -chrM 11385 T T 25 0 25 1 . I -chrM 11386 C C 25 0 25 1 . I -chrM 11387 C C 25 0 25 1 . I -chrM 11388 T T 25 0 25 1 . I -chrM 11389 A A 25 0 25 1 . I -chrM 11390 A A 25 0 25 1 . I -chrM 11391 T T 25 0 25 1 . I -chrM 11392 A A 25 0 25 1 . G -chrM 11393 G G 25 0 25 1 . I -chrM 11394 G G 25 0 25 1 . I -chrM 11395 A A 25 0 25 1 . I -chrM 11396 G G 25 0 25 1 . I -chrM 11397 C C 25 0 25 1 . I -chrM 11398 C C 25 0 25 1 . I -chrM 11399 A A 25 0 25 1 . I -chrM 11400 A A 25 0 25 1 . I -chrM 11401 T T 25 0 25 1 . I -chrM 11402 A A 25 0 25 1 . I -chrM 11403 T T 25 0 25 1 . I -chrM 11404 C C 25 0 25 1 . I -chrM 11405 A A 25 0 25 1 . @ -chrM 11406 C C 25 0 25 1 . I -chrM 11407 C C 25 0 25 1 . I -chrM 11408 A A 19 0 25 1 . 4 -chrM 11409 T T 25 0 25 1 . I -chrM 11410 C C 25 0 25 1 .$ I -chrM 11457 A A 25 0 25 1 ^:. I -chrM 11458 A A 25 0 25 1 . I -chrM 11459 T T 25 0 25 1 . I -chrM 11460 A A 25 0 25 1 . I -chrM 11461 C C 25 0 25 1 . I -chrM 11462 A A 25 0 25 1 . I -chrM 11463 C C 25 0 25 1 . I -chrM 11464 A A 4 0 25 1 N " -chrM 11465 C A 4 4 25 1 N " -chrM 11466 A A 25 0 25 1 . I -chrM 11467 C C 25 0 25 1 . I -chrM 11468 C C 25 0 25 1 . I -chrM 11469 A A 25 0 25 1 . I -chrM 11470 T T 25 0 25 1 . I -chrM 11471 A A 25 0 25 1 . I -chrM 11472 T T 25 0 25 1 . I -chrM 11473 C C 25 0 25 1 . I -chrM 11474 A A 25 0 25 1 . I -chrM 11475 A A 25 0 25 1 . I -chrM 11476 C C 25 0 25 1 . I -chrM 11477 A A 25 0 25 1 . I -chrM 11478 G G 25 0 25 1 . I -chrM 11479 C C 25 0 25 1 . I -chrM 11480 A A 25 0 25 1 . I -chrM 11481 T T 25 0 25 1 . I -chrM 11482 T T 25 0 25 1 . I -chrM 11483 A A 25 0 25 1 . I -chrM 11484 A A 25 0 25 1 . I -chrM 11485 A A 25 0 25 1 . I -chrM 11486 C C 25 0 25 1 . I -chrM 11487 C C 25 0 25 1 . I -chrM 11488 T T 25 0 25 1 . I -chrM 11489 T T 25 0 25 1 . I -chrM 11490 C C 25 0 25 1 . I -chrM 11491 A A 25 0 25 1 . @ -chrM 11492 T T 25 0 25 1 .$ I -chrM 11616 G G 25 0 25 1 ^:, I -chrM 11617 A A 25 0 25 1 , I -chrM 11618 T T 24 0 25 1 , 9 -chrM 11619 C C 25 0 25 1 , I -chrM 11620 T T 25 0 25 1 , I -chrM 11621 A A 25 0 25 1 , I -chrM 11622 G G 25 0 25 1 , I -chrM 11623 A A 25 0 25 1 , I -chrM 11624 A A 25 0 25 1 , I -chrM 11625 A A 25 0 25 1 , I -chrM 11626 C C 25 0 25 1 , I -chrM 11627 A A 25 0 25 1 , I -chrM 11628 G G 25 0 25 1 , I -chrM 11629 A A 25 0 25 1 , I -chrM 11630 A A 25 0 25 1 , I -chrM 11631 A A 25 0 25 1 , I -chrM 11632 C C 25 0 25 1 , I -chrM 11633 T T 25 0 25 1 , I -chrM 11634 T T 25 0 25 1 , I -chrM 11635 A A 25 0 25 1 , I -chrM 11636 A A 25 0 25 1 , I -chrM 11637 T T 25 0 25 1 , I -chrM 11638 A A 25 0 25 1 , I -chrM 11639 T T 25 0 25 1 , I -chrM 11640 T T 25 0 25 1 , I -chrM 11641 T T 25 0 25 1 , I -chrM 11642 C C 25 0 25 1 , I -chrM 11643 T A 4 4 25 1 n " -chrM 11644 T A 4 4 25 1 n " -chrM 11645 A A 25 0 25 1 , I -chrM 11646 T T 25 0 25 1 , I -chrM 11647 T T 25 0 25 1 , I -chrM 11648 T T 25 0 25 1 , I -chrM 11649 A A 25 0 25 1 , I -chrM 11650 C C 25 0 25 1 , I -chrM 11651 C C 25 0 25 1 ,$ I -chrM 11721 A A 25 0 25 1 ^:. I -chrM 11722 G G 25 0 25 1 . I -chrM 11723 G G 25 0 25 1 . I -chrM 11724 A A 25 0 25 1 . I -chrM 11725 T T 25 0 25 1 . I -chrM 11726 A A 25 0 25 1 . I -chrM 11727 G G 25 0 25 1 . I -chrM 11728 G A 4 4 25 1 N " -chrM 11729 A A 4 0 25 1 N " -chrM 11730 G G 25 0 25 1 . I -chrM 11731 C C 25 0 25 1 . I -chrM 11732 T T 25 0 25 1 . I -chrM 11733 A A 25 0 25 1 . I -chrM 11734 T T 25 0 25 1 . I -chrM 11735 C C 25 0 25 1 . I -chrM 11736 C C 25 0 25 1 . I -chrM 11737 G G 25 0 25 1 . I -chrM 11738 T T 25 0 25 1 . I -chrM 11739 T T 25 0 25 1 . I -chrM 11740 G G 25 0 25 1 . I -chrM 11741 G G 25 0 25 1 . I -chrM 11742 T T 25 0 25 1 . I -chrM 11743 C C 25 0 25 1 . I -chrM 11744 T T 25 0 25 1 . I -chrM 11745 T T 25 0 25 1 . I -chrM 11746 A A 25 0 25 1 . I -chrM 11747 G G 25 0 25 1 . I -chrM 11748 G G 25 0 25 1 . I -chrM 11749 A A 25 0 25 1 . F -chrM 11750 A A 25 0 25 1 . I -chrM 11751 C C 25 0 25 1 . I -chrM 11752 C C 25 0 25 1 . I -chrM 11753 A A 25 0 25 1 . H -chrM 11754 A A 25 0 25 1 . : -chrM 11755 A A 21 0 25 1 . 6 -chrM 11756 A A 25 0 25 1 .$ I -chrM 12013 C C 25 0 25 1 ^:, I -chrM 12014 C C 25 0 25 1 , I -chrM 12015 T T 25 0 25 1 , I -chrM 12016 A A 25 0 25 1 , I -chrM 12017 A A 25 0 25 1 , I -chrM 12018 G G 25 0 25 1 , I -chrM 12019 C C 25 0 25 1 , I -chrM 12020 T T 25 0 25 1 , I -chrM 12021 T T 25 0 25 1 , F -chrM 12022 C C 25 0 25 1 , I -chrM 12023 A A 25 0 25 1 , I -chrM 12024 A A 25 0 25 1 , I -chrM 12025 A A 25 0 25 1 , I -chrM 12026 C C 25 0 25 1 , I -chrM 12027 T T 25 0 25 1 , I -chrM 12028 A A 25 0 25 1 , I -chrM 12029 G G 25 0 25 1 , I -chrM 12030 A A 25 0 25 1 , I -chrM 12031 T T 25 0 25 1 , I -chrM 12032 T T 25 0 25 1 , I -chrM 12033 A A 25 0 25 1 , I -chrM 12034 C C 25 0 25 1 , I -chrM 12035 T T 25 0 25 1 , I -chrM 12036 T T 25 0 25 1 , I -chrM 12037 C C 25 0 25 1 , I -chrM 12038 T T 25 0 25 1 , I -chrM 12039 C C 25 0 25 1 , I -chrM 12040 A A 4 0 25 1 n " -chrM 12041 A A 4 0 25 1 n " -chrM 12042 T T 25 0 25 1 , I -chrM 12043 A A 25 0 25 1 , I -chrM 12044 A A 25 0 25 1 , I -chrM 12045 T T 25 0 25 1 , I -chrM 12046 T T 25 0 25 1 , I -chrM 12047 T T 25 0 25 1 , I -chrM 12048 T T 25 0 25 1 ,$ I -chrM 12295 A A 25 0 25 1 ^:. I -chrM 12296 A A 25 0 25 1 . I -chrM 12297 T T 25 0 25 1 . I -chrM 12298 C C 25 0 25 1 . I -chrM 12299 C C 25 0 25 1 . I -chrM 12300 T T 25 0 25 1 . I -chrM 12301 T T 25 0 25 1 . I -chrM 12302 T A 4 4 25 1 N " -chrM 12303 A A 4 0 25 1 N " -chrM 12304 T T 25 0 25 1 . I -chrM 12305 A A 25 0 25 1 . I -chrM 12306 A A 25 0 25 1 . I -chrM 12307 C C 25 0 25 1 . I -chrM 12308 C C 25 0 25 1 . I -chrM 12309 G G 25 0 25 1 . I -chrM 12310 C C 25 0 25 1 . I -chrM 12311 A A 25 0 25 1 . I -chrM 12312 T T 25 0 25 1 . I -chrM 12313 C C 25 0 25 1 . I -chrM 12314 G G 25 0 25 1 . I -chrM 12315 G G 25 0 25 1 . I -chrM 12316 G G 25 0 25 1 . I -chrM 12317 G G 25 0 25 1 . I -chrM 12318 A A 25 0 25 1 . I -chrM 12319 T T 25 0 25 1 . I -chrM 12320 A A 25 0 25 1 . I -chrM 12321 T T 25 0 25 1 . I -chrM 12322 C C 25 0 25 1 . I -chrM 12323 G G 25 0 25 1 . I -chrM 12324 G G 25 0 25 1 . I -chrM 12325 C C 25 0 25 1 . I -chrM 12326 T T 25 0 25 1 . I -chrM 12327 T T 25 0 25 1 . I -chrM 12328 C C 25 0 25 1 . : -chrM 12329 A A 7 0 25 1 . ( -chrM 12330 T T 25 0 25 1 .$ D -chrM 12387 T T 25 0 25 1 ^:, F -chrM 12388 C C 25 0 25 1 , I -chrM 12389 A A 25 0 25 1 , I -chrM 12390 T T 25 0 25 1 , H -chrM 12391 A A 25 0 25 1 , I -chrM 12392 C C 25 0 25 1 , I -chrM 12393 T T 25 0 25 1 , ; -chrM 12394 C C 25 0 25 1 , I -chrM 12395 G G 25 0 25 1 , I -chrM 12396 A A 25 0 25 1 , I -chrM 12397 C C 25 0 25 1 , I -chrM 12398 C C 25 0 25 1 , I -chrM 12399 C C 25 0 25 1 , I -chrM 12400 C C 25 0 25 1 , I -chrM 12401 A A 25 0 25 1 , I -chrM 12402 A A 25 0 25 1 , I -chrM 12403 C C 25 0 25 1 , I -chrM 12404 C C 25 0 25 1 , I -chrM 12405 T T 25 0 25 1 , I -chrM 12406 T T 25 0 25 1 , I -chrM 12407 A A 25 0 25 1 , I -chrM 12408 C C 25 0 25 1 , I -chrM 12409 C C 25 0 25 1 , I -chrM 12410 A A 25 0 25 1 , I -chrM 12411 A A 25 0 25 1 , I -chrM 12412 C C 25 0 25 1 , I -chrM 12413 C C 25 0 25 1 , I -chrM 12414 T A 4 4 25 1 n " -chrM 12415 C A 4 4 25 1 n " -chrM 12416 C C 25 0 25 1 , I -chrM 12417 C C 25 0 25 1 , I -chrM 12418 G G 25 0 25 1 , I -chrM 12419 C C 25 0 25 1 , I -chrM 12420 T T 25 0 25 1 , I -chrM 12421 C C 25 0 25 1 , I -chrM 12422 C C 25 0 25 1 ,$ I -chrM 12584 G G 25 0 25 1 ^:. I -chrM 12585 A A 25 0 25 1 . I -chrM 12586 A A 25 0 25 1 . I -chrM 12587 A A 25 0 25 1 . I -chrM 12588 A A 25 0 25 1 . I -chrM 12589 C C 25 0 25 1 . I -chrM 12590 A A 25 0 25 1 . I -chrM 12591 A A 4 0 25 1 N " -chrM 12592 C A 4 4 25 1 N " -chrM 12593 A A 25 0 25 1 . I -chrM 12594 A A 25 0 25 1 . I -chrM 12595 A A 25 0 25 1 . I -chrM 12596 A A 25 0 25 1 . I -chrM 12597 C C 25 0 25 1 . I -chrM 12598 A A 25 0 25 1 . I -chrM 12599 A A 25 0 25 1 . I -chrM 12600 T T 25 0 25 1 . I -chrM 12601 C C 25 0 25 1 . I -chrM 12602 C C 25 0 25 1 . I -chrM 12603 A A 25 0 25 1 . I -chrM 12604 G G 25 0 25 1 . I -chrM 12605 T T 25 0 25 1 . I -chrM 12606 C C 25 0 25 1 . I -chrM 12607 A A 25 0 25 1 . I -chrM 12608 C C 25 0 25 1 . I -chrM 12609 T T 25 0 25 1 . I -chrM 12610 T T 25 0 25 1 . I -chrM 12611 A A 25 0 25 1 . I -chrM 12612 C C 25 0 25 1 . I -chrM 12613 C C 25 0 25 1 . I -chrM 12614 C C 25 0 25 1 . I -chrM 12615 T T 25 0 25 1 . I -chrM 12616 A A 25 0 25 1 . @ -chrM 12617 T T 25 0 25 1 . I -chrM 12618 G G 25 0 25 1 . I -chrM 12619 C C 25 0 25 1 .$ I -chrM 12988 G G 25 0 25 1 ^:. I -chrM 12989 T T 25 0 25 1 . I -chrM 12990 A A 25 0 25 1 . I -chrM 12991 C C 25 0 25 1 . I -chrM 12992 A A 25 0 25 1 . I -chrM 12993 C C 25 0 25 1 . I -chrM 12994 C C 25 0 25 1 . I -chrM 12995 A A 4 0 25 1 N " -chrM 12996 A A 4 0 25 1 N " -chrM 12997 C C 25 0 25 1 . I -chrM 12998 G G 25 0 25 1 . I -chrM 12999 C C 25 0 25 1 . I -chrM 13000 C C 25 0 25 1 . I -chrM 13001 T T 25 0 25 1 . I -chrM 13002 G G 25 0 25 1 . I -chrM 13003 A A 24 0 25 1 . 9 -chrM 13004 G G 25 0 25 1 . I -chrM 13005 C C 25 0 25 1 . I -chrM 13006 C C 25 0 25 1 . I -chrM 13007 C C 25 0 25 1 . I -chrM 13008 T T 25 0 25 1 . I -chrM 13009 A A 25 0 25 1 . I -chrM 13010 C C 25 0 25 1 . E -chrM 13011 T T 25 0 25 1 . I -chrM 13012 A A 7 0 25 1 . ( -chrM 13013 A A 25 0 25 1 . I -chrM 13014 T T 25 0 25 1 . I -chrM 13015 A A 24 0 25 1 . 9 -chrM 13016 A A 13 0 25 1 . . -chrM 13017 C C 25 0 25 1 . I -chrM 13018 T T 19 0 25 1 . 4 -chrM 13019 C C 25 0 25 1 . I -chrM 13020 T T 25 0 25 1 . I -chrM 13021 C C 25 0 25 1 . I -chrM 13022 A A 11 0 25 1 . , -chrM 13023 T T 25 0 25 1 .$ I -chrM 13560 T T 25 0 25 1 ^:, I -chrM 13561 C C 25 0 25 1 , I -chrM 13562 A A 25 0 25 1 , I -chrM 13563 C C 25 0 25 1 , I -chrM 13564 C C 25 0 25 1 , I -chrM 13565 C C 25 0 25 1 , I -chrM 13566 T T 25 0 25 1 , I -chrM 13567 T T 25 0 25 1 , I -chrM 13568 A A 25 0 25 1 , I -chrM 13569 C C 25 0 25 1 , I -chrM 13570 C C 25 0 25 1 , I -chrM 13571 C C 25 0 25 1 , I -chrM 13572 T T 25 0 25 1 , I -chrM 13573 A A 25 0 25 1 , I -chrM 13574 A A 25 0 25 1 , I -chrM 13575 G G 25 0 25 1 , I -chrM 13576 C C 25 0 25 1 , I -chrM 13577 A A 25 0 25 1 , I -chrM 13578 T T 25 0 25 1 , I -chrM 13579 A A 25 0 25 1 , I -chrM 13580 C C 25 0 25 1 , I -chrM 13581 T T 25 0 25 1 , I -chrM 13582 A A 25 0 25 1 , I -chrM 13583 C C 25 0 25 1 , I -chrM 13584 T T 25 0 25 1 , I -chrM 13585 T T 25 0 25 1 , I -chrM 13586 T T 25 0 25 1 , I -chrM 13587 T A 4 4 25 1 n " -chrM 13588 T A 4 4 25 1 n " -chrM 13589 A A 25 0 25 1 , I -chrM 13590 A A 25 0 25 1 , I -chrM 13591 T T 25 0 25 1 , I -chrM 13592 C C 25 0 25 1 , I -chrM 13593 T T 25 0 25 1 , I -chrM 13594 C C 25 0 25 1 , I -chrM 13595 C C 25 0 25 1 ,$ I -chrM 13783 T T 25 0 25 1 ^:. I -chrM 13784 C C 25 0 25 1 . I -chrM 13785 A A 25 0 25 1 . I -chrM 13786 C C 25 0 25 1 . I -chrM 13787 T T 25 0 25 1 . I -chrM 13788 C C 25 0 25 1 . I -chrM 13789 T T 25 0 25 1 . I -chrM 13790 T A 4 4 25 1 N " -chrM 13791 C A 4 4 25 1 N " -chrM 13792 A A 25 0 25 1 . I -chrM 13793 G G 25 0 25 1 . I -chrM 13794 A A 25 0 25 1 . I -chrM 13795 A A 25 0 25 1 . I -chrM 13796 C C 25 0 25 1 . I -chrM 13797 A A 25 0 25 1 . I -chrM 13798 T T 25 0 25 1 . I -chrM 13799 A A 25 0 25 1 . I -chrM 13800 T T 25 0 25 1 . I -chrM 13801 A A 25 0 25 1 . I -chrM 13802 A A 25 0 25 1 . I -chrM 13803 A A 25 0 25 1 . I -chrM 13804 A A 25 0 25 1 . I -chrM 13805 C C 25 0 25 1 . I -chrM 13806 C C 25 0 25 1 . I -chrM 13807 A A 25 0 25 1 . I -chrM 13808 A A 25 0 25 1 . I -chrM 13809 C C 25 0 25 1 . I -chrM 13810 A A 25 0 25 1 . ? -chrM 13811 T T 25 0 25 1 . I -chrM 13812 A A 25 0 25 1 . C -chrM 13813 A A 25 0 25 1 . C -chrM 13814 C C 25 0 25 1 . I -chrM 13815 C C 25 0 25 1 . I -chrM 13816 T T 25 0 25 1 . I -chrM 13817 C C 25 0 25 1 . I -chrM 13818 C C 25 0 25 1 .$ I -chrM 13855 G G 25 0 25 1 ^:, I -chrM 13856 T T 25 0 25 1 , I -chrM 13857 A A 25 0 25 1 , I -chrM 13858 T T 25 0 25 1 , I -chrM 13859 T T 25 0 25 1 , I -chrM 13860 A A 25 0 25 1 , I -chrM 13861 G G 25 0 25 1 , I -chrM 13862 A A 25 0 25 1 , I -chrM 13863 C C 25 0 25 1 , I -chrM 13864 A A 25 0 25 1 , I -chrM 13865 C C 25 0 25 1 , I -chrM 13866 C C 25 0 25 1 , I -chrM 13867 C C 25 0 25 1 , I -chrM 13868 A A 25 0 25 1 , I -chrM 13869 T T 25 0 25 1 , I -chrM 13870 A A 25 0 25 1 , I -chrM 13871 C C 25 0 25 1 , I -chrM 13872 C C 25 0 25 1 , I -chrM 13873 T T 25 0 25 1 , I -chrM 13874 C C 25 0 25 1 , I -chrM 13875 A A 25 0 25 1 , I -chrM 13876 G G 25 0 25 1 , I -chrM 13877 G G 25 0 25 1 , I -chrM 13878 A A 25 0 25 1 , I -chrM 13879 T T 25 0 25 1 , I -chrM 13880 A A 25 0 25 1 , I -chrM 13881 C C 25 0 25 1 , I -chrM 13882 T A 4 4 25 1 n " -chrM 13883 G A 4 4 25 1 n " -chrM 13884 C C 25 0 25 1 , I -chrM 13885 T T 25 0 25 1 , I -chrM 13886 C C 25 0 25 1 , I -chrM 13887 A A 25 0 25 1 , I -chrM 13888 G G 25 0 25 1 , I -chrM 13889 T T 25 0 25 1 , I -chrM 13890 A A 25 0 25 1 ,$ I -chrM 14023 A A 25 0 25 1 ^:, I -chrM 14024 A A 25 0 25 1 , I -chrM 14025 A A 25 0 25 1 , I -chrM 14026 C C 14 0 25 1 , / -chrM 14027 C C 25 0 25 1 , : -chrM 14028 C C 5 0 25 1 , & -chrM 14029 C C 25 0 25 1 , G -chrM 14030 C C 25 0 25 1 , I -chrM 14031 A A 25 0 25 1 , I -chrM 14032 T T 18 0 25 1 , 3 -chrM 14033 A A 25 0 25 1 , I -chrM 14034 A A 25 0 25 1 , I -chrM 14035 A A 33 0 25 2 ,^:, II +chrM 10926 A A 33 0 25 2 ,$, EI +chrM 10927 C C 30 0 25 1 , I +chrM 10928 G G 30 0 25 1 , I +chrM 10929 G N 0 0 0 1 n " +chrM 10930 A N 0 0 0 1 n " +chrM 10931 A A 30 0 25 1 , I +chrM 10932 T T 30 0 25 1 , I +chrM 10933 A A 30 0 25 1 , I +chrM 10934 C C 30 0 25 1 , I +chrM 10935 T T 30 0 25 1 , I +chrM 10936 A A 30 0 25 1 , I +chrM 10937 C C 30 0 25 1 ,$ 7 +chrM 10991 A A 30 0 25 1 ^:. E +chrM 10992 T T 30 0 25 1 . I +chrM 10993 A A 30 0 25 1 . I +chrM 10994 C C 30 0 25 1 . I +chrM 10995 T T 30 0 25 1 . I +chrM 10996 A A 30 0 25 1 . I +chrM 10997 T T 30 0 25 1 . I +chrM 10998 C N 0 0 0 1 N " +chrM 10999 C N 0 0 0 1 N " +chrM 11000 C C 30 0 25 1 . I +chrM 11001 T T 30 0 25 1 . I +chrM 11002 G G 30 0 25 1 . I +chrM 11003 T T 30 0 25 1 . I +chrM 11004 G G 30 0 25 1 . I +chrM 11005 A A 30 0 25 1 . 2 +chrM 11006 G G 30 0 25 1 . I +chrM 11007 G G 30 0 25 1 . I +chrM 11008 A A 30 0 25 1 . I +chrM 11009 A A 30 0 25 1 . I +chrM 11010 T T 30 0 25 1 . I +chrM 11011 A A 30 0 25 1 . I +chrM 11012 A A 30 0 25 1 . I +chrM 11013 T T 30 0 25 1 . I +chrM 11014 C C 30 0 25 1 . I +chrM 11015 A A 30 0 25 1 . I +chrM 11016 T T 30 0 25 1 . I +chrM 11017 A A 30 0 25 1 . F +chrM 11018 A A 30 0 25 1 . I +chrM 11019 C C 30 0 25 1 . I +chrM 11020 T T 30 0 25 1 . I +chrM 11021 A A 30 0 25 1 . : +chrM 11022 G G 30 0 25 1 . I +chrM 11023 T T 30 0 25 1 . I +chrM 11024 T T 30 0 25 1 . I +chrM 11025 C C 30 0 25 1 . E +chrM 11026 C C 30 0 25 1 .$ B +chrM 11036 C C 30 0 25 1 ^:, E +chrM 11037 G G 30 0 25 1 , I +chrM 11038 A A 30 0 25 1 , I +chrM 11039 C C 30 0 25 1 , I +chrM 11040 A A 30 0 25 1 , I +chrM 11041 A A 30 0 25 1 , I +chrM 11042 A A 30 0 25 1 , I +chrM 11043 C C 30 0 25 1 , I +chrM 11044 C C 30 0 25 1 , I +chrM 11045 G G 30 0 25 1 , I +chrM 11046 A A 30 0 25 1 , I +chrM 11047 T T 30 0 25 1 , I +chrM 11048 C C 30 0 25 1 , I +chrM 11049 T T 30 0 25 1 , I +chrM 11050 A A 30 0 25 1 , I +chrM 11051 A A 30 0 25 1 , I +chrM 11052 A A 30 0 25 1 , I +chrM 11053 A A 30 0 25 1 , I +chrM 11054 T T 30 0 25 1 , I +chrM 11055 C C 30 0 25 1 , I +chrM 11056 A A 30 0 25 1 , I +chrM 11057 C C 30 0 25 1 , I +chrM 11058 T T 30 0 25 1 , I +chrM 11059 T T 30 0 25 1 , I +chrM 11060 A A 30 0 25 1 , I +chrM 11061 T T 30 0 25 1 , I +chrM 11062 T T 30 0 25 1 , I +chrM 11063 G N 0 0 0 1 n " +chrM 11064 C N 0 0 0 1 n " +chrM 11065 A A 30 0 25 1 , I +chrM 11066 T T 30 0 25 1 , I +chrM 11067 A A 30 0 25 1 , I +chrM 11068 C C 30 0 25 1 , I +chrM 11069 T T 30 0 25 1 , I +chrM 11070 C C 30 0 25 1 , E +chrM 11071 C C 30 0 25 1 ,$ A +chrM 11086 A A 30 0 25 1 ^:, E +chrM 11087 G G 30 0 25 1 , 1 +chrM 11088 C N 0 0 0 1 , ' +chrM 11089 C C 30 0 25 1 , = +chrM 11090 C C 30 0 25 1 , D +chrM 11091 T T 30 0 25 1 , 0 +chrM 11092 A A 30 0 25 1 , I +chrM 11093 G G 30 0 25 1 , @ +chrM 11094 T T 30 0 25 1 , 4 +chrM 11095 A A 30 0 25 1 , I +chrM 11096 A A 30 0 25 1 , I +chrM 11097 T T 30 0 25 1 , A +chrM 11098 C C 30 0 25 1 , I +chrM 11099 G G 30 0 25 1 , I +chrM 11100 T T 30 0 25 1 , D +chrM 11101 A A 30 0 25 1 , I +chrM 11102 G G 30 0 25 1 , I +chrM 11103 C C 30 0 25 1 , I +chrM 11104 C C 30 0 25 1 , I +chrM 11105 G G 30 0 25 1 , I +chrM 11106 T T 30 0 25 1 , I +chrM 11107 C C 30 0 25 1 , I +chrM 11108 C C 30 0 25 1 , I +chrM 11109 T T 30 0 25 1 , I +chrM 11110 C C 30 0 25 1 , I +chrM 11111 A A 30 0 25 1 , I +chrM 11112 T T 30 0 25 1 , I +chrM 11113 C N 0 0 0 1 n " +chrM 11114 C N 0 0 0 1 n " +chrM 11115 A A 30 0 25 1 , I +chrM 11116 A A 30 0 25 1 , I +chrM 11117 A A 30 0 25 1 , I +chrM 11118 C C 30 0 25 1 , I +chrM 11119 A A 30 0 25 1 , I +chrM 11120 C C 30 0 25 1 , E +chrM 11121 C C 30 0 25 1 ,$ B +chrM 11375 A A 30 0 25 1 ^:. D +chrM 11376 T T 30 0 25 1 . I +chrM 11377 T T 30 0 25 1 . I +chrM 11378 A A 30 0 25 1 . I +chrM 11379 C C 30 0 25 1 . I +chrM 11380 C C 30 0 25 1 . I +chrM 11381 A A 30 0 25 1 . I +chrM 11382 T N 0 0 0 1 N " +chrM 11383 T N 0 0 0 1 N " +chrM 11384 A A 30 0 25 1 . I +chrM 11385 T T 30 0 25 1 . I +chrM 11386 C C 30 0 25 1 . I +chrM 11387 C C 30 0 25 1 . I +chrM 11388 T T 30 0 25 1 . I +chrM 11389 A A 30 0 25 1 . I +chrM 11390 A A 30 0 25 1 . I +chrM 11391 T T 30 0 25 1 . I +chrM 11392 A A 30 0 25 1 . G +chrM 11393 G G 30 0 25 1 . I +chrM 11394 G G 30 0 25 1 . I +chrM 11395 A A 30 0 25 1 . I +chrM 11396 G G 30 0 25 1 . I +chrM 11397 C C 30 0 25 1 . I +chrM 11398 C C 30 0 25 1 . I +chrM 11399 A A 30 0 25 1 . I +chrM 11400 A A 30 0 25 1 . I +chrM 11401 T T 30 0 25 1 . I +chrM 11402 A A 30 0 25 1 . I +chrM 11403 T T 30 0 25 1 . I +chrM 11404 C C 30 0 25 1 . I +chrM 11405 A A 30 0 25 1 . @ +chrM 11406 C C 30 0 25 1 . I +chrM 11407 C C 30 0 25 1 . I +chrM 11408 A A 30 0 25 1 . 4 +chrM 11409 T T 30 0 25 1 . I +chrM 11410 C C 30 0 25 1 .$ C +chrM 11457 A A 30 0 25 1 ^:. > +chrM 11458 A A 30 0 25 1 . > +chrM 11459 T T 30 0 25 1 . I +chrM 11460 A A 30 0 25 1 . I +chrM 11461 C C 30 0 25 1 . I +chrM 11462 A A 30 0 25 1 . I +chrM 11463 C C 30 0 25 1 . I +chrM 11464 A N 0 0 0 1 N " +chrM 11465 C N 0 0 0 1 N " +chrM 11466 A A 30 0 25 1 . I +chrM 11467 C C 30 0 25 1 . I +chrM 11468 C C 30 0 25 1 . I +chrM 11469 A A 30 0 25 1 . I +chrM 11470 T T 30 0 25 1 . I +chrM 11471 A A 30 0 25 1 . I +chrM 11472 T T 30 0 25 1 . I +chrM 11473 C C 30 0 25 1 . I +chrM 11474 A A 30 0 25 1 . I +chrM 11475 A A 30 0 25 1 . I +chrM 11476 C C 30 0 25 1 . I +chrM 11477 A A 30 0 25 1 . I +chrM 11478 G G 30 0 25 1 . I +chrM 11479 C C 30 0 25 1 . I +chrM 11480 A A 30 0 25 1 . I +chrM 11481 T T 30 0 25 1 . I +chrM 11482 T T 30 0 25 1 . I +chrM 11483 A A 30 0 25 1 . I +chrM 11484 A A 30 0 25 1 . I +chrM 11485 A A 30 0 25 1 . I +chrM 11486 C C 30 0 25 1 . I +chrM 11487 C C 30 0 25 1 . I +chrM 11488 T T 30 0 25 1 . I +chrM 11489 T T 30 0 25 1 . I +chrM 11490 C C 30 0 25 1 . I +chrM 11491 A A 30 0 25 1 . @ +chrM 11492 T T 30 0 25 1 .$ > +chrM 11616 G G 30 0 25 1 ^:, E +chrM 11617 A A 30 0 25 1 , I +chrM 11618 T T 30 0 25 1 , 9 +chrM 11619 C C 30 0 25 1 , I +chrM 11620 T T 30 0 25 1 , I +chrM 11621 A A 30 0 25 1 , I +chrM 11622 G G 30 0 25 1 , I +chrM 11623 A A 30 0 25 1 , I +chrM 11624 A A 30 0 25 1 , I +chrM 11625 A A 30 0 25 1 , I +chrM 11626 C C 30 0 25 1 , I +chrM 11627 A A 30 0 25 1 , I +chrM 11628 G G 30 0 25 1 , I +chrM 11629 A A 30 0 25 1 , I +chrM 11630 A A 30 0 25 1 , I +chrM 11631 A A 30 0 25 1 , I +chrM 11632 C C 30 0 25 1 , I +chrM 11633 T T 30 0 25 1 , I +chrM 11634 T T 30 0 25 1 , I +chrM 11635 A A 30 0 25 1 , I +chrM 11636 A A 30 0 25 1 , I +chrM 11637 T T 30 0 25 1 , I +chrM 11638 A A 30 0 25 1 , I +chrM 11639 T T 30 0 25 1 , I +chrM 11640 T T 30 0 25 1 , I +chrM 11641 T T 30 0 25 1 , I +chrM 11642 C C 30 0 25 1 , I +chrM 11643 T N 0 0 0 1 n " +chrM 11644 T N 0 0 0 1 n " +chrM 11645 A A 30 0 25 1 , I +chrM 11646 T T 30 0 25 1 , I +chrM 11647 T T 30 0 25 1 , I +chrM 11648 T T 30 0 25 1 , I +chrM 11649 A A 30 0 25 1 , I +chrM 11650 C C 30 0 25 1 , E +chrM 11651 C C 30 0 25 1 ,$ B +chrM 11721 A A 30 0 25 1 ^:. E +chrM 11722 G G 30 0 25 1 . I +chrM 11723 G G 30 0 25 1 . I +chrM 11724 A A 30 0 25 1 . I +chrM 11725 T T 30 0 25 1 . I +chrM 11726 A A 30 0 25 1 . I +chrM 11727 G G 30 0 25 1 . I +chrM 11728 G N 0 0 0 1 N " +chrM 11729 A N 0 0 0 1 N " +chrM 11730 G G 30 0 25 1 . I +chrM 11731 C C 30 0 25 1 . I +chrM 11732 T T 30 0 25 1 . I +chrM 11733 A A 30 0 25 1 . I +chrM 11734 T T 30 0 25 1 . I +chrM 11735 C C 30 0 25 1 . I +chrM 11736 C C 30 0 25 1 . I +chrM 11737 G G 30 0 25 1 . I +chrM 11738 T T 30 0 25 1 . I +chrM 11739 T T 30 0 25 1 . I +chrM 11740 G G 30 0 25 1 . I +chrM 11741 G G 30 0 25 1 . I +chrM 11742 T T 30 0 25 1 . I +chrM 11743 C C 30 0 25 1 . I +chrM 11744 T T 30 0 25 1 . I +chrM 11745 T T 30 0 25 1 . I +chrM 11746 A A 30 0 25 1 . I +chrM 11747 G G 30 0 25 1 . I +chrM 11748 G G 30 0 25 1 . I +chrM 11749 A A 30 0 25 1 . F +chrM 11750 A A 30 0 25 1 . I +chrM 11751 C C 30 0 25 1 . I +chrM 11752 C C 30 0 25 1 . I +chrM 11753 A A 30 0 25 1 . > +chrM 11754 A A 30 0 25 1 . : +chrM 11755 A A 30 0 25 1 . 6 +chrM 11756 A A 30 0 25 1 .$ 8 +chrM 12013 C C 30 0 25 1 ^:, > +chrM 12014 C C 30 0 25 1 , > +chrM 12015 T T 30 0 25 1 , I +chrM 12016 A A 30 0 25 1 , I +chrM 12017 A A 30 0 25 1 , I +chrM 12018 G G 30 0 25 1 , I +chrM 12019 C C 30 0 25 1 , I +chrM 12020 T T 30 0 25 1 , I +chrM 12021 T T 30 0 25 1 , F +chrM 12022 C C 30 0 25 1 , I +chrM 12023 A A 30 0 25 1 , I +chrM 12024 A A 30 0 25 1 , I +chrM 12025 A A 30 0 25 1 , I +chrM 12026 C C 30 0 25 1 , I +chrM 12027 T T 30 0 25 1 , I +chrM 12028 A A 30 0 25 1 , I +chrM 12029 G G 30 0 25 1 , I +chrM 12030 A A 30 0 25 1 , I +chrM 12031 T T 30 0 25 1 , I +chrM 12032 T T 30 0 25 1 , I +chrM 12033 A A 30 0 25 1 , I +chrM 12034 C C 30 0 25 1 , I +chrM 12035 T T 30 0 25 1 , I +chrM 12036 T T 30 0 25 1 , I +chrM 12037 C C 30 0 25 1 , I +chrM 12038 T T 30 0 25 1 , I +chrM 12039 C C 30 0 25 1 , I +chrM 12040 A N 0 0 0 1 n " +chrM 12041 A N 0 0 0 1 n " +chrM 12042 T T 30 0 25 1 , I +chrM 12043 A A 30 0 25 1 , I +chrM 12044 A A 30 0 25 1 , I +chrM 12045 T T 30 0 25 1 , E +chrM 12046 T T 30 0 25 1 , B +chrM 12047 T T 30 0 25 1 , A +chrM 12048 T T 30 0 25 1 ,$ ? +chrM 12295 A A 30 0 25 1 ^:. B +chrM 12296 A A 30 0 25 1 . E +chrM 12297 T T 30 0 25 1 . I +chrM 12298 C C 30 0 25 1 . I +chrM 12299 C C 30 0 25 1 . I +chrM 12300 T T 30 0 25 1 . I +chrM 12301 T T 30 0 25 1 . I +chrM 12302 T N 0 0 0 1 N " +chrM 12303 A N 0 0 0 1 N " +chrM 12304 T T 30 0 25 1 . I +chrM 12305 A A 30 0 25 1 . I +chrM 12306 A A 30 0 25 1 . I +chrM 12307 C C 30 0 25 1 . I +chrM 12308 C C 30 0 25 1 . I +chrM 12309 G G 30 0 25 1 . I +chrM 12310 C C 30 0 25 1 . I +chrM 12311 A A 30 0 25 1 . I +chrM 12312 T T 30 0 25 1 . I +chrM 12313 C C 30 0 25 1 . I +chrM 12314 G G 30 0 25 1 . I +chrM 12315 G G 30 0 25 1 . I +chrM 12316 G G 30 0 25 1 . I +chrM 12317 G G 30 0 25 1 . I +chrM 12318 A A 30 0 25 1 . I +chrM 12319 T T 30 0 25 1 . I +chrM 12320 A A 30 0 25 1 . I +chrM 12321 T T 30 0 25 1 . I +chrM 12322 C C 30 0 25 1 . I +chrM 12323 G G 30 0 25 1 . I +chrM 12324 G G 30 0 25 1 . I +chrM 12325 C C 30 0 25 1 . I +chrM 12326 T T 30 0 25 1 . I +chrM 12327 T T 30 0 25 1 . I +chrM 12328 C C 30 0 25 1 . : +chrM 12329 A N 0 0 0 1 . ( +chrM 12330 T T 30 0 25 1 .$ D +chrM 12387 T T 30 0 25 1 ^:, E +chrM 12388 C C 30 0 25 1 , I +chrM 12389 A A 30 0 25 1 , I +chrM 12390 T T 30 0 25 1 , H +chrM 12391 A A 30 0 25 1 , I +chrM 12392 C C 30 0 25 1 , I +chrM 12393 T T 30 0 25 1 , ; +chrM 12394 C C 30 0 25 1 , I +chrM 12395 G G 30 0 25 1 , I +chrM 12396 A A 30 0 25 1 , I +chrM 12397 C C 30 0 25 1 , I +chrM 12398 C C 30 0 25 1 , I +chrM 12399 C C 30 0 25 1 , I +chrM 12400 C C 30 0 25 1 , I +chrM 12401 A A 30 0 25 1 , I +chrM 12402 A A 30 0 25 1 , I +chrM 12403 C C 30 0 25 1 , I +chrM 12404 C C 30 0 25 1 , I +chrM 12405 T T 30 0 25 1 , I +chrM 12406 T T 30 0 25 1 , I +chrM 12407 A A 30 0 25 1 , I +chrM 12408 C C 30 0 25 1 , I +chrM 12409 C C 30 0 25 1 , I +chrM 12410 A A 30 0 25 1 , I +chrM 12411 A A 30 0 25 1 , I +chrM 12412 C C 30 0 25 1 , I +chrM 12413 C C 30 0 25 1 , I +chrM 12414 T N 0 0 0 1 n " +chrM 12415 C N 0 0 0 1 n " +chrM 12416 C C 30 0 25 1 , I +chrM 12417 C C 30 0 25 1 , I +chrM 12418 G G 30 0 25 1 , I +chrM 12419 C C 30 0 25 1 , I +chrM 12420 T T 30 0 25 1 , I +chrM 12421 C C 30 0 25 1 , E +chrM 12422 C C 30 0 25 1 ,$ B +chrM 12584 G G 30 0 25 1 ^:. E +chrM 12585 A A 30 0 25 1 . I +chrM 12586 A A 30 0 25 1 . I +chrM 12587 A A 30 0 25 1 . I +chrM 12588 A A 30 0 25 1 . I +chrM 12589 C C 30 0 25 1 . I +chrM 12590 A A 30 0 25 1 . I +chrM 12591 A N 0 0 0 1 N " +chrM 12592 C N 0 0 0 1 N " +chrM 12593 A A 30 0 25 1 . I +chrM 12594 A A 30 0 25 1 . I +chrM 12595 A A 30 0 25 1 . I +chrM 12596 A A 30 0 25 1 . I +chrM 12597 C C 30 0 25 1 . I +chrM 12598 A A 30 0 25 1 . I +chrM 12599 A A 30 0 25 1 . I +chrM 12600 T T 30 0 25 1 . I +chrM 12601 C C 30 0 25 1 . I +chrM 12602 C C 30 0 25 1 . I +chrM 12603 A A 30 0 25 1 . I +chrM 12604 G G 30 0 25 1 . I +chrM 12605 T T 30 0 25 1 . I +chrM 12606 C C 30 0 25 1 . I +chrM 12607 A A 30 0 25 1 . I +chrM 12608 C C 30 0 25 1 . I +chrM 12609 T T 30 0 25 1 . I +chrM 12610 T T 30 0 25 1 . I +chrM 12611 A A 30 0 25 1 . I +chrM 12612 C C 30 0 25 1 . I +chrM 12613 C C 30 0 25 1 . I +chrM 12614 C C 30 0 25 1 . I +chrM 12615 T T 30 0 25 1 . I +chrM 12616 A A 30 0 25 1 . @ +chrM 12617 T T 30 0 25 1 . I +chrM 12618 G G 30 0 25 1 . I +chrM 12619 C C 30 0 25 1 .$ > +chrM 12988 G G 30 0 25 1 ^:. E +chrM 12989 T T 30 0 25 1 . I +chrM 12990 A A 30 0 25 1 . I +chrM 12991 C C 30 0 25 1 . I +chrM 12992 A A 30 0 25 1 . I +chrM 12993 C C 30 0 25 1 . I +chrM 12994 C C 30 0 25 1 . I +chrM 12995 A N 0 0 0 1 N " +chrM 12996 A N 0 0 0 1 N " +chrM 12997 C C 30 0 25 1 . I +chrM 12998 G G 30 0 25 1 . I +chrM 12999 C C 30 0 25 1 . I +chrM 13000 C C 30 0 25 1 . I +chrM 13001 T T 30 0 25 1 . I +chrM 13002 G G 30 0 25 1 . I +chrM 13003 A A 30 0 25 1 . 9 +chrM 13004 G G 30 0 25 1 . I +chrM 13005 C C 30 0 25 1 . I +chrM 13006 C C 30 0 25 1 . I +chrM 13007 C C 30 0 25 1 . I +chrM 13008 T T 30 0 25 1 . I +chrM 13009 A A 30 0 25 1 . I +chrM 13010 C C 30 0 25 1 . E +chrM 13011 T T 30 0 25 1 . I +chrM 13012 A N 0 0 0 1 . ( +chrM 13013 A A 30 0 25 1 . I +chrM 13014 T T 30 0 25 1 . I +chrM 13015 A A 30 0 25 1 . 9 +chrM 13016 A A 30 0 25 1 . . +chrM 13017 C C 30 0 25 1 . I +chrM 13018 T T 30 0 25 1 . 4 +chrM 13019 C C 30 0 25 1 . I +chrM 13020 T T 30 0 25 1 . I +chrM 13021 C C 30 0 25 1 . I +chrM 13022 A N 0 0 0 1 . , +chrM 13023 T T 30 0 25 1 .$ > +chrM 13560 T T 30 0 25 1 ^:, E +chrM 13561 C C 30 0 25 1 , I +chrM 13562 A A 30 0 25 1 , I +chrM 13563 C C 30 0 25 1 , I +chrM 13564 C C 30 0 25 1 , I +chrM 13565 C C 30 0 25 1 , I +chrM 13566 T T 30 0 25 1 , I +chrM 13567 T T 30 0 25 1 , I +chrM 13568 A A 30 0 25 1 , I +chrM 13569 C C 30 0 25 1 , I +chrM 13570 C C 30 0 25 1 , I +chrM 13571 C C 30 0 25 1 , I +chrM 13572 T T 30 0 25 1 , I +chrM 13573 A A 30 0 25 1 , I +chrM 13574 A A 30 0 25 1 , I +chrM 13575 G G 30 0 25 1 , I +chrM 13576 C C 30 0 25 1 , I +chrM 13577 A A 30 0 25 1 , I +chrM 13578 T T 30 0 25 1 , I +chrM 13579 A A 30 0 25 1 , I +chrM 13580 C C 30 0 25 1 , I +chrM 13581 T T 30 0 25 1 , I +chrM 13582 A A 30 0 25 1 , I +chrM 13583 C C 30 0 25 1 , I +chrM 13584 T T 30 0 25 1 , I +chrM 13585 T T 30 0 25 1 , I +chrM 13586 T T 30 0 25 1 , I +chrM 13587 T N 0 0 0 1 n " +chrM 13588 T N 0 0 0 1 n " +chrM 13589 A A 30 0 25 1 , I +chrM 13590 A A 30 0 25 1 , I +chrM 13591 T T 30 0 25 1 , I +chrM 13592 C C 30 0 25 1 , I +chrM 13593 T T 30 0 25 1 , I +chrM 13594 C C 30 0 25 1 , E +chrM 13595 C C 30 0 25 1 ,$ A +chrM 13783 T T 30 0 25 1 ^:. E +chrM 13784 C C 30 0 25 1 . I +chrM 13785 A A 30 0 25 1 . I +chrM 13786 C C 30 0 25 1 . I +chrM 13787 T T 30 0 25 1 . I +chrM 13788 C C 30 0 25 1 . I +chrM 13789 T T 30 0 25 1 . I +chrM 13790 T N 0 0 0 1 N " +chrM 13791 C N 0 0 0 1 N " +chrM 13792 A A 30 0 25 1 . I +chrM 13793 G G 30 0 25 1 . I +chrM 13794 A A 30 0 25 1 . I +chrM 13795 A A 30 0 25 1 . I +chrM 13796 C C 30 0 25 1 . I +chrM 13797 A A 30 0 25 1 . I +chrM 13798 T T 30 0 25 1 . I +chrM 13799 A A 30 0 25 1 . I +chrM 13800 T T 30 0 25 1 . I +chrM 13801 A A 30 0 25 1 . I +chrM 13802 A A 30 0 25 1 . I +chrM 13803 A A 30 0 25 1 . I +chrM 13804 A A 30 0 25 1 . I +chrM 13805 C C 30 0 25 1 . I +chrM 13806 C C 30 0 25 1 . I +chrM 13807 A A 30 0 25 1 . I +chrM 13808 A A 30 0 25 1 . I +chrM 13809 C C 30 0 25 1 . I +chrM 13810 A A 30 0 25 1 . ? +chrM 13811 T T 30 0 25 1 . I +chrM 13812 A A 30 0 25 1 . C +chrM 13813 A A 30 0 25 1 . C +chrM 13814 C C 30 0 25 1 . I +chrM 13815 C C 30 0 25 1 . I +chrM 13816 T T 30 0 25 1 . I +chrM 13817 C C 30 0 25 1 . E +chrM 13818 C C 30 0 25 1 .$ B +chrM 13855 G G 30 0 25 1 ^:, E +chrM 13856 T T 30 0 25 1 , I +chrM 13857 A A 30 0 25 1 , I +chrM 13858 T T 30 0 25 1 , I +chrM 13859 T T 30 0 25 1 , I +chrM 13860 A A 30 0 25 1 , I +chrM 13861 G G 30 0 25 1 , I +chrM 13862 A A 30 0 25 1 , I +chrM 13863 C C 30 0 25 1 , I +chrM 13864 A A 30 0 25 1 , I +chrM 13865 C C 30 0 25 1 , I +chrM 13866 C C 30 0 25 1 , I +chrM 13867 C C 30 0 25 1 , I +chrM 13868 A A 30 0 25 1 , I +chrM 13869 T T 30 0 25 1 , I +chrM 13870 A A 30 0 25 1 , I +chrM 13871 C C 30 0 25 1 , I +chrM 13872 C C 30 0 25 1 , I +chrM 13873 T T 30 0 25 1 , I +chrM 13874 C C 30 0 25 1 , I +chrM 13875 A A 30 0 25 1 , I +chrM 13876 G G 30 0 25 1 , I +chrM 13877 G G 30 0 25 1 , I +chrM 13878 A A 30 0 25 1 , I +chrM 13879 T T 30 0 25 1 , I +chrM 13880 A A 30 0 25 1 , I +chrM 13881 C C 30 0 25 1 , I +chrM 13882 T N 0 0 0 1 n " +chrM 13883 G N 0 0 0 1 n " +chrM 13884 C C 30 0 25 1 , I +chrM 13885 T T 30 0 25 1 , I +chrM 13886 C C 30 0 25 1 , I +chrM 13887 A A 30 0 25 1 , I +chrM 13888 G G 30 0 25 1 , I +chrM 13889 T T 30 0 25 1 , I +chrM 13890 A A 30 0 25 1 ,$ E +chrM 14023 A A 30 0 25 1 ^:, A +chrM 14024 A A 30 0 25 1 , B +chrM 14025 A A 30 0 25 1 , E +chrM 14026 C C 30 0 25 1 , / +chrM 14027 C C 30 0 25 1 , : +chrM 14028 C N 0 0 0 1 , & +chrM 14029 C C 30 0 25 1 , G +chrM 14030 C C 30 0 25 1 , I +chrM 14031 A A 30 0 25 1 , I +chrM 14032 T T 30 0 25 1 , 3 +chrM 14033 A A 30 0 25 1 , I +chrM 14034 A A 30 0 25 1 , I +chrM 14035 A A 33 0 25 2 ,^:, IE chrM 14036 T T 33 0 25 2 ,, ;; chrM 14037 A A 33 0 25 2 ,, II chrM 14038 G G 33 0 25 2 ,, II @@ -2874,207 +2874,207 @@ chrM 14046 T T 33 0 25 2 ,, II chrM 14047 T T 33 0 25 2 ,, II chrM 14048 T T 33 0 25 2 ,, II chrM 14049 T T 33 0 25 2 ,, II -chrM 14050 G G 19 0 25 2 n, "I -chrM 14051 A A 28 0 25 2 n, "I +chrM 14050 G G 30 0 25 2 n, "I +chrM 14051 A A 30 0 25 2 n, "I chrM 14052 A A 33 0 25 2 ,, II chrM 14053 G G 33 0 25 2 ,, II chrM 14054 A A 33 0 25 2 ,, II chrM 14055 A A 33 0 25 2 ,, II chrM 14056 A A 33 0 25 2 ,, II chrM 14057 A A 33 0 25 2 ,, II -chrM 14058 C C 33 0 25 2 ,$, II -chrM 14059 C C 25 0 25 1 , I -chrM 14060 C C 25 0 25 1 , I -chrM 14061 C C 25 0 25 1 , I -chrM 14062 A A 28 0 25 2 n^:, "I -chrM 14063 C C 4 0 25 2 n, "+ +chrM 14058 C C 33 0 25 2 ,$, >I +chrM 14059 C C 30 0 25 1 , I +chrM 14060 C C 30 0 25 1 , I +chrM 14061 C C 30 0 25 1 , I +chrM 14062 A A 30 0 25 2 n^:, "E +chrM 14063 C N 0 0 0 2 n, "+ chrM 14064 A A 33 0 25 2 ,, II chrM 14065 A A 33 0 25 2 ,, II chrM 14066 A A 33 0 25 2 ,, II chrM 14067 A A 33 0 25 2 ,, II chrM 14068 C C 33 0 25 2 ,, I1 chrM 14069 T T 33 0 25 2 ,, II -chrM 14070 A A 33 0 25 2 ,$, II -chrM 14071 A A 25 0 25 1 , I -chrM 14072 C C 25 0 25 1 , I -chrM 14073 A A 25 0 25 1 , I -chrM 14074 A A 25 0 25 1 , I -chrM 14075 C C 25 0 25 1 , I -chrM 14076 A A 25 0 25 1 , I -chrM 14077 A A 25 0 25 1 , I -chrM 14078 A A 25 0 25 1 , I -chrM 14079 A A 25 0 25 1 , I -chrM 14080 A A 25 0 25 1 , I -chrM 14081 T T 25 0 25 1 , I -chrM 14082 A A 25 0 25 1 , I -chrM 14083 A A 25 0 25 1 , I -chrM 14084 C C 25 0 25 1 , I -chrM 14085 A A 25 0 25 1 , I -chrM 14086 C C 25 0 25 1 , I -chrM 14087 T T 25 0 25 1 , I -chrM 14088 C C 25 0 25 1 , I -chrM 14089 A A 4 0 25 1 n " -chrM 14090 A A 4 0 25 1 n " -chrM 14091 A A 25 0 25 1 , I -chrM 14092 A A 25 0 25 1 , I -chrM 14093 T T 25 0 25 1 , I -chrM 14094 A A 25 0 25 1 , I -chrM 14095 A A 25 0 25 1 , I -chrM 14096 A A 25 0 25 1 , I -chrM 14097 C C 25 0 25 1 ,$ I -chrM 14239 T T 25 0 25 1 ^:, I -chrM 14240 T T 25 0 25 1 , I -chrM 14241 T T 25 0 25 1 , I -chrM 14242 A A 25 0 25 1 , I -chrM 14243 T T 25 0 25 1 , I -chrM 14244 T T 25 0 25 1 , B -chrM 14245 G G 25 0 25 1 , I -chrM 14246 A A 25 0 25 1 , I -chrM 14247 C C 25 0 25 1 , I -chrM 14248 C C 25 0 25 1 , I -chrM 14249 T T 25 0 25 1 , I -chrM 14250 A A 25 0 25 1 , I -chrM 14251 C C 25 0 25 1 , I -chrM 14252 C C 25 0 25 1 , I -chrM 14253 A A 25 0 25 1 , I -chrM 14254 G G 25 0 25 1 , I -chrM 14255 C C 25 0 25 1 , I -chrM 14256 C C 25 0 25 1 , I -chrM 14257 C C 25 0 25 1 , I -chrM 14258 C C 25 0 25 1 , I -chrM 14259 C C 25 0 25 1 , I -chrM 14260 T T 25 0 25 1 , I -chrM 14261 C C 25 0 25 1 , I -chrM 14262 A A 25 0 25 1 , I -chrM 14263 A A 25 0 25 1 , I -chrM 14264 A A 25 0 25 1 , I -chrM 14265 C C 25 0 25 1 , I -chrM 14266 A A 4 0 25 1 n " -chrM 14267 T A 4 4 25 1 n " -chrM 14268 T T 25 0 25 1 , I -chrM 14269 T T 25 0 25 1 , I -chrM 14270 C C 25 0 25 1 , I -chrM 14271 A A 25 0 25 1 , I -chrM 14272 T T 25 0 25 1 , I -chrM 14273 C C 25 0 25 1 , I -chrM 14274 A A 25 0 25 1 ,$ I -chrM 14463 C C 25 0 25 1 ^:, I -chrM 14464 T T 25 0 25 1 , G -chrM 14465 G G 25 0 25 1 , I -chrM 14466 C C 25 0 25 1 , I -chrM 14467 C C 25 0 25 1 , I -chrM 14468 T T 25 0 25 1 , ; -chrM 14469 C C 25 0 25 1 , I -chrM 14470 T T 25 0 25 1 , I -chrM 14471 T T 23 0 25 1 , 8 -chrM 14472 C C 25 0 25 1 , I -chrM 14473 A A 25 0 25 1 , I -chrM 14474 T T 25 0 25 1 , I -chrM 14475 T T 25 0 25 1 , I -chrM 14476 C C 25 0 25 1 , I -chrM 14477 A A 25 0 25 1 , I -chrM 14478 C C 25 0 25 1 , I -chrM 14479 G G 25 0 25 1 , I -chrM 14480 T T 25 0 25 1 , I -chrM 14481 A A 25 0 25 1 , I -chrM 14482 G G 25 0 25 1 , I -chrM 14483 G G 25 0 25 1 , I -chrM 14484 A A 25 0 25 1 , I -chrM 14485 C C 25 0 25 1 , I -chrM 14486 G G 25 0 25 1 , I -chrM 14487 C C 25 0 25 1 , I -chrM 14488 G G 25 0 25 1 , I -chrM 14489 G G 25 0 25 1 , I -chrM 14490 C A 4 4 25 1 n " -chrM 14491 C A 4 4 25 1 n " -chrM 14492 T T 25 0 25 1 , I -chrM 14493 C C 25 0 25 1 , I -chrM 14494 T T 25 0 25 1 , I -chrM 14495 A A 25 0 25 1 , I -chrM 14496 C C 25 0 25 1 , I -chrM 14497 T T 25 0 25 1 , I -chrM 14498 A A 25 0 25 1 ,$ I -chrM 14866 A A 25 0 25 1 ^:, I -chrM 14867 A A 21 0 25 1 , 6 -chrM 14868 A A 25 0 25 1 , I -chrM 14869 G G 18 0 25 1 , 3 -chrM 14870 A A 11 0 25 1 , , -chrM 14871 C C 6 0 25 1 , ' -chrM 14872 A A 24 0 25 1 , 9 -chrM 14873 T T 19 0 25 1 , 4 -chrM 14874 C C 25 0 25 1 , I -chrM 14875 C C 25 0 25 1 , I -chrM 14876 T T 25 0 25 1 , A -chrM 14877 A A 25 0 25 1 , I -chrM 14878 G G 7 0 25 1 , ( -chrM 14879 G G 25 0 25 1 , I -chrM 14880 A A 25 0 25 1 , A -chrM 14881 C C 25 0 25 1 , I -chrM 14882 T T 25 0 25 1 , G -chrM 14883 C C 25 0 25 1 , I -chrM 14884 C C 9 0 25 1 , * -chrM 14885 T T 19 0 25 1 , 4 -chrM 14886 C C 25 0 25 1 , I -chrM 14887 C C 25 0 25 1 , I -chrM 14888 T T 25 0 25 1 , F -chrM 14889 C C 25 0 25 1 , I -chrM 14890 C C 25 0 25 1 , I -chrM 14891 T T 25 0 25 1 , I -chrM 14892 G G 25 0 25 1 , I -chrM 14893 A A 4 0 25 1 n " -chrM 14894 T A 4 4 25 1 n " -chrM 14895 C C 25 0 25 1 , I -chrM 14896 T T 25 0 25 1 , I -chrM 14897 T T 25 0 25 1 , I -chrM 14898 G G 25 0 25 1 , I -chrM 14899 C C 25 0 25 1 , I -chrM 14900 T T 25 0 25 1 , I -chrM 14901 C C 25 0 25 1 ,$ I -chrM 14956 A A 25 0 25 1 ^:. I -chrM 14957 C C 25 0 25 1 . I -chrM 14958 C C 25 0 25 1 . I -chrM 14959 C C 25 0 25 1 . I -chrM 14960 C C 25 0 25 1 . I -chrM 14961 A A 25 0 25 1 . I -chrM 14962 G G 25 0 25 1 . I -chrM 14963 C A 4 4 25 1 N " -chrM 14964 T A 4 4 25 1 N " -chrM 14965 A A 25 0 25 1 . I -chrM 14966 A A 25 0 25 1 . I -chrM 14967 C C 25 0 25 1 . I -chrM 14968 C C 25 0 25 1 . I -chrM 14969 C C 25 0 25 1 . I -chrM 14970 T T 25 0 25 1 . I -chrM 14971 C C 25 0 25 1 . I -chrM 14972 T T 25 0 25 1 . I -chrM 14973 C C 25 0 25 1 . I -chrM 14974 A A 25 0 25 1 . I -chrM 14975 G G 25 0 25 1 . I -chrM 14976 C C 25 0 25 1 . I -chrM 14977 A A 21 0 25 1 . 6 -chrM 14978 C C 25 0 25 1 . I -chrM 14979 T T 25 0 25 1 . I -chrM 14980 C C 25 0 25 1 . I -chrM 14981 C C 25 0 25 1 . I -chrM 14982 C C 25 0 25 1 . I -chrM 14983 C C 25 0 25 1 . I -chrM 14984 C C 25 0 25 1 . I -chrM 14985 T T 25 0 25 1 . I -chrM 14986 C C 25 0 25 1 . I -chrM 14987 A A 20 0 25 1 . 5 -chrM 14988 T T 25 0 25 1 . I -chrM 14989 A A 12 0 25 1 . - -chrM 14990 T T 25 0 25 1 . I -chrM 14991 T T 25 0 25 1 .$ I -chrM 15012 G G 25 0 25 1 ^:. I -chrM 15013 T T 25 0 25 1 . I -chrM 15014 T T 33 0 25 2 .^:, II +chrM 14070 A A 33 0 25 2 ,$, >I +chrM 14071 A A 30 0 25 1 , I +chrM 14072 C C 30 0 25 1 , I +chrM 14073 A A 30 0 25 1 , I +chrM 14074 A A 30 0 25 1 , I +chrM 14075 C C 30 0 25 1 , I +chrM 14076 A A 30 0 25 1 , I +chrM 14077 A A 30 0 25 1 , I +chrM 14078 A A 30 0 25 1 , I +chrM 14079 A A 30 0 25 1 , I +chrM 14080 A A 30 0 25 1 , I +chrM 14081 T T 30 0 25 1 , I +chrM 14082 A A 30 0 25 1 , I +chrM 14083 A A 30 0 25 1 , I +chrM 14084 C C 30 0 25 1 , I +chrM 14085 A A 30 0 25 1 , I +chrM 14086 C C 30 0 25 1 , I +chrM 14087 T T 30 0 25 1 , I +chrM 14088 C C 30 0 25 1 , I +chrM 14089 A N 0 0 0 1 n " +chrM 14090 A N 0 0 0 1 n " +chrM 14091 A A 30 0 25 1 , I +chrM 14092 A A 30 0 25 1 , I +chrM 14093 T T 30 0 25 1 , I +chrM 14094 A A 30 0 25 1 , I +chrM 14095 A A 30 0 25 1 , I +chrM 14096 A A 30 0 25 1 , I +chrM 14097 C C 30 0 25 1 ,$ C +chrM 14239 T T 30 0 25 1 ^:, ; +chrM 14240 T T 30 0 25 1 , ; +chrM 14241 T T 30 0 25 1 , > +chrM 14242 A A 30 0 25 1 , I +chrM 14243 T T 30 0 25 1 , I +chrM 14244 T T 30 0 25 1 , B +chrM 14245 G G 30 0 25 1 , I +chrM 14246 A A 30 0 25 1 , I +chrM 14247 C C 30 0 25 1 , I +chrM 14248 C C 30 0 25 1 , I +chrM 14249 T T 30 0 25 1 , I +chrM 14250 A A 30 0 25 1 , I +chrM 14251 C C 30 0 25 1 , I +chrM 14252 C C 30 0 25 1 , I +chrM 14253 A A 30 0 25 1 , I +chrM 14254 G G 30 0 25 1 , I +chrM 14255 C C 30 0 25 1 , I +chrM 14256 C C 30 0 25 1 , I +chrM 14257 C C 30 0 25 1 , I +chrM 14258 C C 30 0 25 1 , I +chrM 14259 C C 30 0 25 1 , I +chrM 14260 T T 30 0 25 1 , I +chrM 14261 C C 30 0 25 1 , I +chrM 14262 A A 30 0 25 1 , I +chrM 14263 A A 30 0 25 1 , I +chrM 14264 A A 30 0 25 1 , I +chrM 14265 C C 30 0 25 1 , I +chrM 14266 A N 0 0 0 1 n " +chrM 14267 T N 0 0 0 1 n " +chrM 14268 T T 30 0 25 1 , I +chrM 14269 T T 30 0 25 1 , I +chrM 14270 C C 30 0 25 1 , I +chrM 14271 A A 30 0 25 1 , I +chrM 14272 T T 30 0 25 1 , I +chrM 14273 C C 30 0 25 1 , I +chrM 14274 A A 30 0 25 1 ,$ E +chrM 14463 C C 30 0 25 1 ^:, E +chrM 14464 T T 30 0 25 1 , G +chrM 14465 G G 30 0 25 1 , I +chrM 14466 C C 30 0 25 1 , I +chrM 14467 C C 30 0 25 1 , I +chrM 14468 T T 30 0 25 1 , ; +chrM 14469 C C 30 0 25 1 , I +chrM 14470 T T 30 0 25 1 , I +chrM 14471 T T 30 0 25 1 , 8 +chrM 14472 C C 30 0 25 1 , I +chrM 14473 A A 30 0 25 1 , I +chrM 14474 T T 30 0 25 1 , I +chrM 14475 T T 30 0 25 1 , I +chrM 14476 C C 30 0 25 1 , I +chrM 14477 A A 30 0 25 1 , I +chrM 14478 C C 30 0 25 1 , I +chrM 14479 G G 30 0 25 1 , I +chrM 14480 T T 30 0 25 1 , I +chrM 14481 A A 30 0 25 1 , I +chrM 14482 G G 30 0 25 1 , I +chrM 14483 G G 30 0 25 1 , I +chrM 14484 A A 30 0 25 1 , I +chrM 14485 C C 30 0 25 1 , I +chrM 14486 G G 30 0 25 1 , I +chrM 14487 C C 30 0 25 1 , I +chrM 14488 G G 30 0 25 1 , I +chrM 14489 G G 30 0 25 1 , I +chrM 14490 C N 0 0 0 1 n " +chrM 14491 C N 0 0 0 1 n " +chrM 14492 T T 30 0 25 1 , I +chrM 14493 C C 30 0 25 1 , I +chrM 14494 T T 30 0 25 1 , I +chrM 14495 A A 30 0 25 1 , I +chrM 14496 C C 30 0 25 1 , I +chrM 14497 T T 30 0 25 1 , I +chrM 14498 A A 30 0 25 1 ,$ E +chrM 14866 A A 30 0 25 1 ^:, A +chrM 14867 A A 30 0 25 1 , 6 +chrM 14868 A A 30 0 25 1 , E +chrM 14869 G G 30 0 25 1 , 3 +chrM 14870 A N 0 0 0 1 , , +chrM 14871 C N 0 0 0 1 , ' +chrM 14872 A A 30 0 25 1 , 9 +chrM 14873 T T 30 0 25 1 , 4 +chrM 14874 C C 30 0 25 1 , I +chrM 14875 C C 30 0 25 1 , I +chrM 14876 T T 30 0 25 1 , A +chrM 14877 A A 30 0 25 1 , I +chrM 14878 G N 0 0 0 1 , ( +chrM 14879 G G 30 0 25 1 , I +chrM 14880 A A 30 0 25 1 , A +chrM 14881 C C 30 0 25 1 , I +chrM 14882 T T 30 0 25 1 , G +chrM 14883 C C 30 0 25 1 , I +chrM 14884 C N 0 0 0 1 , * +chrM 14885 T T 30 0 25 1 , 4 +chrM 14886 C C 30 0 25 1 , I +chrM 14887 C C 30 0 25 1 , I +chrM 14888 T T 30 0 25 1 , F +chrM 14889 C C 30 0 25 1 , I +chrM 14890 C C 30 0 25 1 , I +chrM 14891 T T 30 0 25 1 , I +chrM 14892 G G 30 0 25 1 , I +chrM 14893 A N 0 0 0 1 n " +chrM 14894 T N 0 0 0 1 n " +chrM 14895 C C 30 0 25 1 , I +chrM 14896 T T 30 0 25 1 , I +chrM 14897 T T 30 0 25 1 , I +chrM 14898 G G 30 0 25 1 , I +chrM 14899 C C 30 0 25 1 , I +chrM 14900 T T 30 0 25 1 , I +chrM 14901 C C 30 0 25 1 ,$ > +chrM 14956 A A 30 0 25 1 ^:. D +chrM 14957 C C 30 0 25 1 . I +chrM 14958 C C 30 0 25 1 . I +chrM 14959 C C 30 0 25 1 . I +chrM 14960 C C 30 0 25 1 . I +chrM 14961 A A 30 0 25 1 . I +chrM 14962 G G 30 0 25 1 . I +chrM 14963 C N 0 0 0 1 N " +chrM 14964 T N 0 0 0 1 N " +chrM 14965 A A 30 0 25 1 . I +chrM 14966 A A 30 0 25 1 . I +chrM 14967 C C 30 0 25 1 . I +chrM 14968 C C 30 0 25 1 . I +chrM 14969 C C 30 0 25 1 . I +chrM 14970 T T 30 0 25 1 . I +chrM 14971 C C 30 0 25 1 . I +chrM 14972 T T 30 0 25 1 . I +chrM 14973 C C 30 0 25 1 . I +chrM 14974 A A 30 0 25 1 . I +chrM 14975 G G 30 0 25 1 . I +chrM 14976 C C 30 0 25 1 . I +chrM 14977 A A 30 0 25 1 . 6 +chrM 14978 C C 30 0 25 1 . I +chrM 14979 T T 30 0 25 1 . I +chrM 14980 C C 30 0 25 1 . I +chrM 14981 C C 30 0 25 1 . I +chrM 14982 C C 30 0 25 1 . I +chrM 14983 C C 30 0 25 1 . I +chrM 14984 C C 30 0 25 1 . I +chrM 14985 T T 30 0 25 1 . I +chrM 14986 C C 30 0 25 1 . I +chrM 14987 A A 30 0 25 1 . 5 +chrM 14988 T T 30 0 25 1 . I +chrM 14989 A N 0 0 0 1 . - +chrM 14990 T T 30 0 25 1 . E +chrM 14991 T T 30 0 25 1 .$ B +chrM 15012 G G 30 0 25 1 ^:. E +chrM 15013 T T 30 0 25 1 . I +chrM 15014 T T 33 0 25 2 .^:, I> chrM 15015 T T 33 0 25 2 ., I8 chrM 15016 G G 33 0 25 2 ., IA chrM 15017 C C 33 0 25 2 ., II chrM 15018 C C 33 0 25 2 ., II -chrM 15019 T T 19 0 25 2 N, ": -chrM 15020 A A 29 0 25 2 N, "I +chrM 15019 T T 30 0 25 2 N, ": +chrM 15020 A A 30 0 25 2 N, "I chrM 15021 C C 33 0 25 2 ., II chrM 15022 G G 33 0 25 2 ., II chrM 15023 C C 33 0 25 2 ., II @@ -3095,192 +3095,192 @@ chrM 15037 A A 33 0 25 2 ., 6I chrM 15038 T T 33 0 25 2 ., II chrM 15039 T T 33 0 25 2 ., II chrM 15040 C C 33 0 25 2 ., II -chrM 15041 C C 19 0 25 2 .n I" -chrM 15042 C C 19 0 25 2 .n I" +chrM 15041 C C 30 0 25 2 .n I" +chrM 15042 C C 30 0 25 2 .n I" chrM 15043 A A 33 0 25 2 ., 1I chrM 15044 A A 33 0 25 2 ., CI chrM 15045 C C 33 0 25 2 ., II chrM 15046 A A 33 0 25 2 ., =I chrM 15047 A A 33 0 25 2 .$, 3I -chrM 15048 A A 25 0 25 1 , I -chrM 15049 C C 25 0 25 1 ,$ I -chrM 15080 T T 25 0 25 1 ^:, H -chrM 15081 C C 25 0 25 1 , I -chrM 15082 C C 25 0 25 1 , I -chrM 15083 T T 25 0 25 1 , I -chrM 15084 G G 25 0 25 1 , I -chrM 15085 A A 25 0 25 1 , I -chrM 15086 T T 25 0 25 1 , F -chrM 15087 C C 25 0 25 1 , I -chrM 15088 C C 25 0 25 1 , I -chrM 15089 T T 25 0 25 1 , A -chrM 15090 A A 25 0 25 1 , I -chrM 15091 G G 25 0 25 1 , H -chrM 15092 C C 25 0 25 1 , I -chrM 15093 A A 25 0 25 1 , I -chrM 15094 C C 25 0 25 1 , I -chrM 15095 T T 25 0 25 1 , I -chrM 15096 C C 25 0 25 1 , I -chrM 15097 A A 25 0 25 1 , I -chrM 15098 T T 25 0 25 1 , I -chrM 15099 C C 25 0 25 1 , I -chrM 15100 C C 25 0 25 1 , I -chrM 15101 C C 25 0 25 1 , I -chrM 15102 C C 25 0 25 1 , I -chrM 15103 A A 25 0 25 1 , I -chrM 15104 C C 25 0 25 1 , I -chrM 15105 C C 25 0 25 1 , I -chrM 15106 C C 25 0 25 1 , I -chrM 15107 T A 4 4 25 1 n " -chrM 15108 C A 4 4 25 1 n " -chrM 15109 C C 25 0 25 1 , I -chrM 15110 A A 25 0 25 1 , I -chrM 15111 C C 25 0 25 1 , I -chrM 15112 A A 25 0 25 1 , I -chrM 15113 T T 25 0 25 1 , I -chrM 15114 A A 25 0 25 1 , I -chrM 15115 T T 25 0 25 1 ,$ I -chrM 15275 T T 25 0 25 1 ^:. I -chrM 15276 C C 25 0 25 1 . I -chrM 15277 A A 25 0 25 1 . I -chrM 15278 T T 25 0 25 1 . I -chrM 15279 T T 25 0 25 1 . I -chrM 15280 T T 25 0 25 1 . I -chrM 15281 T T 25 0 25 1 . I -chrM 15282 T A 4 4 25 1 N " -chrM 15283 A A 4 0 25 1 N " -chrM 15284 T T 25 0 25 1 . I -chrM 15285 A A 25 0 25 1 . I -chrM 15286 C C 25 0 25 1 . I -chrM 15287 C C 25 0 25 1 . I -chrM 15288 A A 25 0 25 1 . I -chrM 15289 C C 25 0 25 1 . I -chrM 15290 T T 25 0 25 1 . I -chrM 15291 C C 25 0 25 1 . I -chrM 15292 G G 25 0 25 1 . I -chrM 15293 C C 25 0 25 1 . I -chrM 15294 A A 25 0 25 1 . I -chrM 15295 A A 25 0 25 1 . I -chrM 15296 G G 25 0 25 1 . I -chrM 15297 C C 25 0 25 1 . I -chrM 15298 A A 25 0 25 1 . I -chrM 15299 C C 25 0 25 1 . I -chrM 15300 C C 25 0 25 1 . I -chrM 15301 A A 25 0 25 1 . @ -chrM 15302 T T 25 0 25 1 . I -chrM 15303 C C 25 0 25 1 . = -chrM 15304 G G 25 0 25 1 . I -chrM 15305 A A 22 0 25 1 . 7 -chrM 15306 A A 24 0 25 1 . 9 -chrM 15307 A A 25 0 25 1 . I -chrM 15308 A A 21 0 25 1 . 6 -chrM 15309 C C 25 0 25 1 . I -chrM 15310 A A 25 0 25 1 .$ I -chrM 15338 T T 25 0 25 1 ^:, E -chrM 15339 A A 25 0 25 1 , I -chrM 15340 T T 25 0 25 1 , I -chrM 15341 A A 25 0 25 1 , I -chrM 15342 T T 25 0 25 1 , ? -chrM 15343 C C 12 0 25 1 , - -chrM 15344 G G 25 0 25 1 , I -chrM 15345 C C 25 0 25 1 , I -chrM 15346 A A 25 0 25 1 , I -chrM 15347 C C 25 0 25 1 , I -chrM 15348 A A 25 0 25 1 , I -chrM 15349 T T 25 0 25 1 , A -chrM 15350 T T 25 0 25 1 , I -chrM 15351 A A 25 0 25 1 , I -chrM 15352 C C 25 0 25 1 , I -chrM 15353 C C 25 0 25 1 , I -chrM 15354 C C 25 0 25 1 , I -chrM 15355 T T 25 0 25 1 , I -chrM 15356 G G 25 0 25 1 , I -chrM 15357 G G 25 0 25 1 , I -chrM 15358 T T 25 0 25 1 , I -chrM 15359 C C 25 0 25 1 , I -chrM 15360 T T 25 0 25 1 , I -chrM 15361 T T 25 0 25 1 , I -chrM 15362 G G 25 0 25 1 , I -chrM 15363 T T 25 0 25 1 , I -chrM 15364 A A 25 0 25 1 , I -chrM 15365 A A 4 0 25 1 n " -chrM 15366 A A 4 0 25 1 n " -chrM 15367 C C 25 0 25 1 , I -chrM 15368 C C 25 0 25 1 , I -chrM 15369 A A 25 0 25 1 , I -chrM 15370 G G 25 0 25 1 , I -chrM 15371 A A 25 0 25 1 , I -chrM 15372 A A 25 0 25 1 , I -chrM 15373 A A 25 0 25 1 ,$ I -chrM 15787 A A 25 0 25 1 ^:, I -chrM 15788 T T 25 0 25 1 , = -chrM 15789 C C 25 0 25 1 , I -chrM 15790 C C 25 0 25 1 , I -chrM 15791 T T 12 0 25 1 , - -chrM 15792 C C 25 0 25 1 , I -chrM 15793 G G 25 0 25 1 , I -chrM 15794 C C 25 0 25 1 , H -chrM 15795 T T 24 0 25 1 , 9 -chrM 15796 C C 25 0 25 1 , I -chrM 15797 C C 25 0 25 1 , I -chrM 15798 G G 25 0 25 1 , I -chrM 15799 G G 25 0 25 1 , I -chrM 15800 G G 25 0 25 1 , I -chrM 15801 C C 25 0 25 1 , I -chrM 15802 C C 25 0 25 1 , I -chrM 15803 C C 25 0 25 1 , I -chrM 15804 A A 25 0 25 1 , I -chrM 15805 T T 25 0 25 1 , D -chrM 15806 C C 25 0 25 1 , I -chrM 15807 C C 25 0 25 1 , I -chrM 15808 A A 25 0 25 1 , I -chrM 15809 A A 25 0 25 1 , I -chrM 15810 A A 25 0 25 1 , I -chrM 15811 C C 25 0 25 1 , I -chrM 15812 G G 25 0 25 1 , I -chrM 15813 T T 25 0 25 1 , I -chrM 15814 G A 4 4 25 1 n " -chrM 15815 G A 4 4 25 1 n " -chrM 15816 G G 25 0 25 1 , I -chrM 15817 G G 25 0 25 1 , I -chrM 15818 G G 25 0 25 1 , I -chrM 15819 T T 25 0 25 1 , I -chrM 15820 T T 25 0 25 1 , I -chrM 15821 T T 25 0 25 1 , I -chrM 15822 C C 25 0 25 1 ,$ I -chrM 16613 G G 25 0 25 1 ^:. I -chrM 16614 C C 25 0 25 1 . I -chrM 16615 A A 25 0 25 1 . I -chrM 16616 T T 25 0 25 1 . I -chrM 16617 C C 25 0 25 1 . I -chrM 16618 C C 25 0 25 1 . I -chrM 16619 C C 25 0 25 1 . I -chrM 16620 C A 4 4 25 1 N " -chrM 16621 C A 4 4 25 1 N " -chrM 16622 T T 25 0 25 1 . I -chrM 16623 A A 25 0 25 1 . I -chrM 16624 G G 25 0 25 1 . I -chrM 16625 A A 25 0 25 1 . @ -chrM 16626 T T 25 0 25 1 . I -chrM 16627 C C 25 0 25 1 . I -chrM 16628 T T 25 0 25 1 . I -chrM 16629 A A 25 0 25 1 . I -chrM 16630 A A 10 0 25 1 . + -chrM 16631 T T 25 0 25 1 . I -chrM 16632 T T 25 0 25 1 . I -chrM 16633 T T 25 0 25 1 . I -chrM 16634 T T 25 0 25 1 . I -chrM 16635 C C 25 0 25 1 . I -chrM 16636 T T 25 0 25 1 . I -chrM 16637 A A 23 0 25 1 . 8 -chrM 16638 A A 25 0 25 1 . H -chrM 16639 A A 23 0 25 1 . 8 -chrM 16640 T T 25 0 25 1 . I -chrM 16641 C C 25 0 25 1 . I -chrM 16642 T T 25 0 25 1 . I -chrM 16643 G G 25 0 25 1 . I -chrM 16644 T T 25 0 25 1 . I -chrM 16645 C C 25 0 25 1 . I -chrM 16646 A A 25 0 25 1 . I -chrM 16647 A A 25 0 25 1 . C -chrM 16648 C C 25 0 25 1 .$ I +chrM 15048 A A 30 0 25 1 , I +chrM 15049 C C 30 0 25 1 ,$ E +chrM 15080 T T 30 0 25 1 ^:, E +chrM 15081 C C 30 0 25 1 , I +chrM 15082 C C 30 0 25 1 , I +chrM 15083 T T 30 0 25 1 , I +chrM 15084 G G 30 0 25 1 , I +chrM 15085 A A 30 0 25 1 , I +chrM 15086 T T 30 0 25 1 , F +chrM 15087 C C 30 0 25 1 , I +chrM 15088 C C 30 0 25 1 , I +chrM 15089 T T 30 0 25 1 , A +chrM 15090 A A 30 0 25 1 , I +chrM 15091 G G 30 0 25 1 , H +chrM 15092 C C 30 0 25 1 , I +chrM 15093 A A 30 0 25 1 , I +chrM 15094 C C 30 0 25 1 , I +chrM 15095 T T 30 0 25 1 , I +chrM 15096 C C 30 0 25 1 , I +chrM 15097 A A 30 0 25 1 , I +chrM 15098 T T 30 0 25 1 , I +chrM 15099 C C 30 0 25 1 , I +chrM 15100 C C 30 0 25 1 , I +chrM 15101 C C 30 0 25 1 , I +chrM 15102 C C 30 0 25 1 , I +chrM 15103 A A 30 0 25 1 , I +chrM 15104 C C 30 0 25 1 , I +chrM 15105 C C 30 0 25 1 , I +chrM 15106 C C 30 0 25 1 , I +chrM 15107 T N 0 0 0 1 n " +chrM 15108 C N 0 0 0 1 n " +chrM 15109 C C 30 0 25 1 , I +chrM 15110 A A 30 0 25 1 , I +chrM 15111 C C 30 0 25 1 , I +chrM 15112 A A 30 0 25 1 , I +chrM 15113 T T 30 0 25 1 , I +chrM 15114 A A 30 0 25 1 , I +chrM 15115 T T 30 0 25 1 ,$ E +chrM 15275 T T 30 0 25 1 ^:. D +chrM 15276 C C 30 0 25 1 . I +chrM 15277 A A 30 0 25 1 . I +chrM 15278 T T 30 0 25 1 . I +chrM 15279 T T 30 0 25 1 . I +chrM 15280 T T 30 0 25 1 . I +chrM 15281 T T 30 0 25 1 . I +chrM 15282 T N 0 0 0 1 N " +chrM 15283 A N 0 0 0 1 N " +chrM 15284 T T 30 0 25 1 . I +chrM 15285 A A 30 0 25 1 . I +chrM 15286 C C 30 0 25 1 . I +chrM 15287 C C 30 0 25 1 . I +chrM 15288 A A 30 0 25 1 . I +chrM 15289 C C 30 0 25 1 . I +chrM 15290 T T 30 0 25 1 . I +chrM 15291 C C 30 0 25 1 . I +chrM 15292 G G 30 0 25 1 . I +chrM 15293 C C 30 0 25 1 . I +chrM 15294 A A 30 0 25 1 . I +chrM 15295 A A 30 0 25 1 . I +chrM 15296 G G 30 0 25 1 . I +chrM 15297 C C 30 0 25 1 . I +chrM 15298 A A 30 0 25 1 . I +chrM 15299 C C 30 0 25 1 . I +chrM 15300 C C 30 0 25 1 . I +chrM 15301 A A 30 0 25 1 . @ +chrM 15302 T T 30 0 25 1 . I +chrM 15303 C C 30 0 25 1 . = +chrM 15304 G G 30 0 25 1 . I +chrM 15305 A A 30 0 25 1 . 7 +chrM 15306 A A 30 0 25 1 . 9 +chrM 15307 A A 30 0 25 1 . I +chrM 15308 A A 30 0 25 1 . 6 +chrM 15309 C C 30 0 25 1 . I +chrM 15310 A A 30 0 25 1 .$ > +chrM 15338 T T 30 0 25 1 ^:, E +chrM 15339 A A 30 0 25 1 , I +chrM 15340 T T 30 0 25 1 , I +chrM 15341 A A 30 0 25 1 , I +chrM 15342 T T 30 0 25 1 , ? +chrM 15343 C N 0 0 0 1 , - +chrM 15344 G G 30 0 25 1 , I +chrM 15345 C C 30 0 25 1 , I +chrM 15346 A A 30 0 25 1 , I +chrM 15347 C C 30 0 25 1 , I +chrM 15348 A A 30 0 25 1 , I +chrM 15349 T T 30 0 25 1 , A +chrM 15350 T T 30 0 25 1 , I +chrM 15351 A A 30 0 25 1 , I +chrM 15352 C C 30 0 25 1 , I +chrM 15353 C C 30 0 25 1 , I +chrM 15354 C C 30 0 25 1 , I +chrM 15355 T T 30 0 25 1 , I +chrM 15356 G G 30 0 25 1 , I +chrM 15357 G G 30 0 25 1 , I +chrM 15358 T T 30 0 25 1 , I +chrM 15359 C C 30 0 25 1 , I +chrM 15360 T T 30 0 25 1 , I +chrM 15361 T T 30 0 25 1 , I +chrM 15362 G G 30 0 25 1 , I +chrM 15363 T T 30 0 25 1 , I +chrM 15364 A A 30 0 25 1 , I +chrM 15365 A N 0 0 0 1 n " +chrM 15366 A N 0 0 0 1 n " +chrM 15367 C C 30 0 25 1 , I +chrM 15368 C C 30 0 25 1 , I +chrM 15369 A A 30 0 25 1 , I +chrM 15370 G G 30 0 25 1 , I +chrM 15371 A A 30 0 25 1 , > +chrM 15372 A A 30 0 25 1 , ; +chrM 15373 A A 30 0 25 1 ,$ : +chrM 15787 A A 30 0 25 1 ^:, E +chrM 15788 T T 30 0 25 1 , = +chrM 15789 C C 30 0 25 1 , I +chrM 15790 C C 30 0 25 1 , I +chrM 15791 T N 0 0 0 1 , - +chrM 15792 C C 30 0 25 1 , I +chrM 15793 G G 30 0 25 1 , I +chrM 15794 C C 30 0 25 1 , H +chrM 15795 T T 30 0 25 1 , 9 +chrM 15796 C C 30 0 25 1 , I +chrM 15797 C C 30 0 25 1 , I +chrM 15798 G G 30 0 25 1 , I +chrM 15799 G G 30 0 25 1 , I +chrM 15800 G G 30 0 25 1 , I +chrM 15801 C C 30 0 25 1 , I +chrM 15802 C C 30 0 25 1 , I +chrM 15803 C C 30 0 25 1 , I +chrM 15804 A A 30 0 25 1 , I +chrM 15805 T T 30 0 25 1 , D +chrM 15806 C C 30 0 25 1 , I +chrM 15807 C C 30 0 25 1 , I +chrM 15808 A A 30 0 25 1 , I +chrM 15809 A A 30 0 25 1 , I +chrM 15810 A A 30 0 25 1 , I +chrM 15811 C C 30 0 25 1 , I +chrM 15812 G G 30 0 25 1 , I +chrM 15813 T T 30 0 25 1 , I +chrM 15814 G N 0 0 0 1 n " +chrM 15815 G N 0 0 0 1 n " +chrM 15816 G G 30 0 25 1 , I +chrM 15817 G G 30 0 25 1 , I +chrM 15818 G G 30 0 25 1 , I +chrM 15819 T T 30 0 25 1 , I +chrM 15820 T T 30 0 25 1 , I +chrM 15821 T T 30 0 25 1 , I +chrM 15822 C C 30 0 25 1 ,$ E +chrM 16613 G G 30 0 25 1 ^:. E +chrM 16614 C C 30 0 25 1 . I +chrM 16615 A A 30 0 25 1 . I +chrM 16616 T T 30 0 25 1 . I +chrM 16617 C C 30 0 25 1 . I +chrM 16618 C C 30 0 25 1 . I +chrM 16619 C C 30 0 25 1 . I +chrM 16620 C N 0 0 0 1 N " +chrM 16621 C N 0 0 0 1 N " +chrM 16622 T T 30 0 25 1 . I +chrM 16623 A A 30 0 25 1 . I +chrM 16624 G G 30 0 25 1 . I +chrM 16625 A A 30 0 25 1 . @ +chrM 16626 T T 30 0 25 1 . I +chrM 16627 C C 30 0 25 1 . I +chrM 16628 T T 30 0 25 1 . I +chrM 16629 A A 30 0 25 1 . I +chrM 16630 A N 0 0 0 1 . + +chrM 16631 T T 30 0 25 1 . I +chrM 16632 T T 30 0 25 1 . I +chrM 16633 T T 30 0 25 1 . I +chrM 16634 T T 30 0 25 1 . I +chrM 16635 C C 30 0 25 1 . I +chrM 16636 T T 30 0 25 1 . I +chrM 16637 A A 30 0 25 1 . 8 +chrM 16638 A A 30 0 25 1 . H +chrM 16639 A A 30 0 25 1 . 8 +chrM 16640 T T 30 0 25 1 . I +chrM 16641 C C 30 0 25 1 . I +chrM 16642 T T 30 0 25 1 . I +chrM 16643 G G 30 0 25 1 . I +chrM 16644 T T 30 0 25 1 . I +chrM 16645 C C 30 0 25 1 . I +chrM 16646 A A 30 0 25 1 . I +chrM 16647 A A 30 0 25 1 . C +chrM 16648 C C 30 0 25 1 .$ > --- a/test-data/bam_to_sam_out2.sam +++ b/test-data/bam_to_sam_out2.sam @@ -1,10 +1,10 @@ HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 Binary file test-data/sam_merge_out2.bam has changed --- a/tools/samtools/bam_to_sam.py +++ b/tools/samtools/bam_to_sam.py @@ -24,12 +24,51 @@ def __main__(): ( options, args ) = parser.parse_args() tmp_dir = tempfile.mkdtemp() + try: # exit if input file empty if os.path.getsize( options.input1 ) == 0: raise Exception, 'Initial BAM file empty' + # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command + # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted + # into memory ( controlled by option -m ). + tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir ) + tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name + tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name + tmp_sorted_aligns_file.close() + command = 'samtools sort %s %s' % ( options.input1, tmp_sorted_aligns_file_base ) + tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + # exit if sorted BAM file empty + if os.path.getsize( tmp_sorted_aligns_file_name) == 0: + raise Exception, 'Intermediate sorted BAM file empty' + except Exception, e: + #clean up temp files + if os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + stop_err( 'Error sorting alignments from (%s), %s' % ( options.input1, str( e ) ) ) + + + try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o %s %s' % ( options.output1, options.input1 ) + command = 'samtools view -o %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/bam_to_sam.xml +++ b/tools/samtools/bam_to_sam.xml @@ -3,7 +3,11 @@ <requirement type="package">samtools</requirement></requirements><description>converts BAM format to SAM format</description> - <command interpreter="python">bam_to_sam.py --input1=$input1 --output1=$output1</command> + <command interpreter="python"> + bam_to_sam.py + --input1=$input1 + --output1=$output1 + </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /></inputs> @@ -14,18 +18,18 @@ <test><param name="input1" value="1.bam" ftype="bam" /> - <output name="output1" file="bam_to_sam_out1.sam" /> + <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /></test><test><param name="input1" value="3.bam" ftype="bam" /> - <param name="output1" file="bam_to_sam_out2.sam" /> + <param name="output1" file="bam_to_sam_out2.sam" sorted="True" /></test></tests><help> --- a/tools/samtools/sam_pileup.xml +++ b/tools/samtools/sam_pileup.xml @@ -5,32 +5,32 @@ </requirements><command interpreter="python"> sam_pileup.py - --input1=$input1 - --output=$output1 - --ref=$refOrHistory.reference - #if $refOrHistory.reference == "history": - --ownFile=$refOrHistory.ownFile - #else: - --ownFile="None" - #end if - --dbkey=${input1.metadata.dbkey} - --indexDir=${GALAXY_DATA_INDEX_DIR} - --bamIndex=${input1.metadata.bam_index} - --lastCol=$lastCol - --indels=$indels - --mapCap=$mapCap - --consensus=$c.consensus - #if $c.consensus == "yes": - --theta=$c.theta - --hapNum=$c.hapNum - --fraction=$c.fraction - --phredProb=$c.phredProb - #else: - --theta="None" - --hapNum="None" - --fraction="None" - --phredProb="None" - #end if + --input1=$input1 + --output=$output1 + --ref=$refOrHistory.reference + #if $refOrHistory.reference == "history": + --ownFile=$refOrHistory.ownFile + #else: + --ownFile="None" + #end if + --dbkey=${input1.metadata.dbkey} + --indexDir=${GALAXY_DATA_INDEX_DIR} + --bamIndex=${input1.metadata.bam_index} + --lastCol=$lastCol + --indels=$indels + --mapCap=$mapCap + --consensus=$c.consensus + #if $c.consensus == "yes": + --theta=$c.theta + --hapNum=$c.hapNum + --fraction=$c.fraction + --phredProb=$c.phredProb + #else: + --theta="None" + --hapNum="None" + --fraction="None" + --phredProb="None" + #end if </command><inputs><conditional name="refOrHistory"> @@ -80,7 +80,7 @@ <param name="reference" value="history" /> @@ -95,7 +95,7 @@ <test><param name="reference" value="indexed" /> Binary file test-data/sam_to_bam_out1.bam has changed

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galaxy-dist commit 2875445df990: merge
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289249827 18000 # Node ID 2875445df9906828bc804e9b0923160f902b3fac # Parent 43c1f36a8e4e3f9aa62dc9bc144e54b8312364bf # Parent 2c2baca255289cd48ecb806cfb0ea6468d489bde merge

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galaxy-dist commit eee0e1d344d2: Update Tophat and Cufflinks tool wrappers and functional tests to support Tophat version 1.1.* This breaks support for Tophat versions 1.0.* and earlier.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289247694 18000 # Node ID eee0e1d344d21de7fb079fcccc3df8e251d1e025 # Parent 1ebd342fb4eb29c095b19a960503402f75cbe944 Update Tophat and Cufflinks tool wrappers and functional tests to support Tophat version 1.1.* This breaks support for Tophat versions 1.0.* and earlier. --- a/test-data/tophat_out2.wig +++ /dev/null @@ -1,175 +0,0 @@ -track type=bedGraph name="TopHat - read coverage" -test_chromosome 0 52 0 -test_chromosome 52 53 1 -test_chromosome 53 54 2 -test_chromosome 54 55 3 -test_chromosome 55 57 4 -test_chromosome 57 58 6 -test_chromosome 58 60 7 -test_chromosome 60 65 8 -test_chromosome 65 70 9 -test_chromosome 70 71 10 -test_chromosome 71 72 11 -test_chromosome 72 75 12 -test_chromosome 75 77 13 -test_chromosome 77 79 15 -test_chromosome 79 82 16 -test_chromosome 82 85 17 -test_chromosome 85 87 19 -test_chromosome 87 88 20 -test_chromosome 88 90 21 -test_chromosome 90 91 22 -test_chromosome 91 93 23 -test_chromosome 93 95 26 -test_chromosome 95 97 28 -test_chromosome 97 99 30 -test_chromosome 99 100 31 -test_chromosome 100 101 35 -test_chromosome 101 102 36 -test_chromosome 102 105 38 -test_chromosome 105 106 39 -test_chromosome 106 107 40 -test_chromosome 107 112 43 -test_chromosome 112 114 44 -test_chromosome 114 118 45 -test_chromosome 118 121 46 -test_chromosome 121 122 48 -test_chromosome 122 124 50 -test_chromosome 124 126 53 -test_chromosome 126 129 54 -test_chromosome 129 130 53 -test_chromosome 130 131 55 -test_chromosome 131 132 57 -test_chromosome 132 133 55 -test_chromosome 133 134 54 -test_chromosome 134 135 55 -test_chromosome 135 136 54 -test_chromosome 136 137 56 -test_chromosome 137 138 57 -test_chromosome 138 141 60 -test_chromosome 141 147 62 -test_chromosome 147 148 61 -test_chromosome 148 150 62 -test_chromosome 150 152 61 -test_chromosome 152 153 60 -test_chromosome 153 154 61 -test_chromosome 154 155 63 -test_chromosome 155 156 64 -test_chromosome 156 158 65 -test_chromosome 158 159 66 -test_chromosome 159 160 68 -test_chromosome 160 161 67 -test_chromosome 161 163 68 -test_chromosome 163 164 69 -test_chromosome 164 165 71 -test_chromosome 165 167 73 -test_chromosome 167 168 74 -test_chromosome 168 169 72 -test_chromosome 169 170 75 -test_chromosome 170 171 73 -test_chromosome 171 172 74 -test_chromosome 172 174 75 -test_chromosome 174 175 77 -test_chromosome 175 176 74 -test_chromosome 176 177 73 -test_chromosome 177 181 71 -test_chromosome 181 182 70 -test_chromosome 182 183 67 -test_chromosome 183 184 68 -test_chromosome 184 189 69 -test_chromosome 189 193 68 -test_chromosome 193 194 69 -test_chromosome 194 195 71 -test_chromosome 195 196 72 -test_chromosome 196 197 70 -test_chromosome 197 199 68 -test_chromosome 199 200 66 -test_chromosome 200 201 67 -test_chromosome 201 202 66 -test_chromosome 202 204 65 -test_chromosome 204 205 67 -test_chromosome 205 207 65 -test_chromosome 207 211 66 -test_chromosome 211 213 65 -test_chromosome 213 216 64 -test_chromosome 216 220 62 -test_chromosome 220 224 63 -test_chromosome 224 225 64 -test_chromosome 225 228 66 -test_chromosome 228 229 65 -test_chromosome 229 230 62 -test_chromosome 230 231 61 -test_chromosome 231 232 60 -test_chromosome 232 234 59 -test_chromosome 234 237 58 -test_chromosome 237 238 57 -test_chromosome 238 239 55 -test_chromosome 239 240 53 -test_chromosome 240 241 50 -test_chromosome 241 242 51 -test_chromosome 242 243 52 -test_chromosome 243 244 53 -test_chromosome 244 246 50 -test_chromosome 246 247 52 -test_chromosome 247 249 50 -test_chromosome 249 250 47 -test_chromosome 250 349 0 -test_chromosome 349 350 1 -test_chromosome 350 351 49 -test_chromosome 351 352 51 -test_chromosome 352 353 53 -test_chromosome 353 354 54 -test_chromosome 354 357 55 -test_chromosome 357 358 56 -test_chromosome 358 361 55 -test_chromosome 361 362 57 -test_chromosome 362 365 56 -test_chromosome 365 366 57 -test_chromosome 366 368 58 -test_chromosome 368 369 57 -test_chromosome 369 372 56 -test_chromosome 372 375 59 -test_chromosome 375 378 60 -test_chromosome 378 379 59 -test_chromosome 379 380 57 -test_chromosome 380 381 56 -test_chromosome 381 382 54 -test_chromosome 382 384 53 -test_chromosome 384 386 52 -test_chromosome 386 387 51 -test_chromosome 387 388 50 -test_chromosome 388 390 48 -test_chromosome 390 395 47 -test_chromosome 395 396 45 -test_chromosome 396 398 44 -test_chromosome 398 399 43 -test_chromosome 399 400 42 -test_chromosome 400 402 1 -test_chromosome 402 500 0 -test_chromosome 500 508 39 -test_chromosome 508 509 38 -test_chromosome 509 510 37 -test_chromosome 510 511 36 -test_chromosome 511 516 35 -test_chromosome 516 517 33 -test_chromosome 517 518 31 -test_chromosome 518 521 29 -test_chromosome 521 522 26 -test_chromosome 522 524 25 -test_chromosome 524 525 24 -test_chromosome 525 526 22 -test_chromosome 526 527 20 -test_chromosome 527 528 18 -test_chromosome 528 529 17 -test_chromosome 529 530 16 -test_chromosome 530 532 15 -test_chromosome 532 534 14 -test_chromosome 534 536 13 -test_chromosome 536 540 11 -test_chromosome 540 541 10 -test_chromosome 541 543 9 -test_chromosome 543 544 8 -test_chromosome 544 545 7 -test_chromosome 545 547 6 -test_chromosome 547 549 3 -test_chromosome 549 549 2 --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -10,9 +10,8 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) - parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) - parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) + parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is BAM.' ) parser.add_option( '', '--own-file', dest='own_file', help='' ) parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' ) parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ @@ -186,33 +185,14 @@ def __main__(): tmp_stderr.close() if returncode != 0: raise Exception, stderr + + # TODO: look for errors in program output. + + # Copy output files from tmp directory to specified files. + shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) + shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.bam" ), options.accepted_hits_output_file ) except Exception, e: - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) - stop_err( 'Error in tophat:\n' + str( e ) ) - - # TODO: look for errors in program output. - - # Postprocessing: copy output files from tmp directory to specified files. Also need to remove header lines from SAM file. - try: - try: - shutil.copyfile( os.path.join( tmp_output_dir, "coverage.wig" ), options.coverage_output_file ) - shutil.copyfile( os.path.join( tmp_output_dir, "junctions.bed" ), options.junctions_output_file ) - - # Remove headers from SAM file in place. - in_header = True # Headers always at start of file. - for line in fileinput.input( os.path.join( tmp_output_dir, "accepted_hits.sam" ), inplace=1 ): - if in_header and line.startswith("@"): - continue - else: - in_header = False - sys.stdout.write( line ) - - # Copy SAM File. - shutil.copyfile( os.path.join( tmp_output_dir, "accepted_hits.sam" ), options.accepted_hits_output_file ) - except Exception, e: - stop_err( 'Error in tophat:\n' + str( e ) ) + stop_err( 'Error in tophat:\n' + str( e ) ) finally: # Clean up temp dirs if os.path.exists( tmp_index_dir ): --- a/test-data/tophat_out3.bed +++ /dev/null @@ -1,3 +0,0 @@ -track name=junctions description="TopHat junctions" -test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 -test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -33,8 +33,8 @@ </command><inputs><param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> - <param format="sam" name="aligned_reads1" type="data" label="SAM file of aligned RNA-Seq reads" help=""/> - <param format="sam" name="aligned_reads2" type="data" label="SAM file of aligned RNA-Seq reads" help=""/> + <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> + <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/><param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/><param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="0" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> --- /dev/null +++ b/test-data/tophat_out1.bed @@ -0,0 +1,3 @@ +track name=junctions description="TopHat junctions" +test_chromosome 180 402 JUNC00000001 46 + 180 402 255,0,0 2 70,52 0,170 +test_chromosome 349 550 JUNC00000002 38 + 349 550 255,0,0 2 51,50 0,151 --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -23,7 +23,7 @@ #end if </command><inputs> - <param format="sam" name="input" type="data" label="SAM file of aligned RNA-Seq reads" help=""/> + <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/><param name="max_intron_len" type="integer" value="300000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" label="Pre MRNA Fraction" help=""/> --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -1,15 +1,14 @@ -<tool id="tophat" name="Tophat" version="1.1.1"> +<tool id="tophat" name="Tophat" version="1.1.2"><description>Find splice junctions using RNA-seq data</description><requirements><requirement type="package">tophat</requirement></requirements><command interpreter="python"> tophat_wrapper.py - ## Change this to accomodate the number of threads you have available. + ## Change this to accommodate the number of threads you have available. --num-threads="4" ## Provide outputs. - --coverage-output=$coverage --junctions-output=$junctions --hits-output=$accepted_hits @@ -338,9 +337,8 @@ </inputs><outputs> - <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> - <data format="bedgraph" name="coverage" label="${tool.name} on ${on_string}: coverage"/><data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/></outputs><tests> @@ -367,9 +365,9 @@ <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="preSet"/> - <output name="accepted_hits" file="tophat_out1.sam" sort="True"/> - <output name="coverage" file="tophat_out2.wig"/> - <output name="junctions" file="tophat_out3.bed"/> + <output name="junctions" file="tophat_out1.bed"/> +  + <output name="accepted_hits" file="tophat_out2.bam" lines_diff="100000"/></test><!-- <test><param name="genomeSource" value="history"/> @@ -451,15 +449,13 @@ Tophat accepts files in Sanger FASTQ for **Outputs** -Tophat produces three output files: +Tophat produces two output files: -- coverage.wig -- A UCSC BedGraph_ wigglegram track, showing the depth of coverage at each position, including the spliced read alignments. -- accepted_hits.sam -- A list of read alignments in SAM_ format. -- junctions.bed -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. - -.. _BedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html -.. _SAM: http://samtools.sourceforge.net/ +- junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. +- accepted_hits -- A list of read alignments in BAM_ format. + .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 +.. _BAM: http://samtools.sourceforge.net/ ------- --- a/test-data/tophat_out1.sam +++ /dev/null @@ -1,179 +0,0 @@ -test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_104_274_1c 73 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 NH:i:1 -test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_111_268_d 73 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_11_190_1a 99 test_chromosome 61 255 75M = 166 0 GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_128_252_36 137 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_150_290_0 73 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_151_286_e 137 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_151_297_1d 137 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_16_194_10 163 test_chromosome 66 255 75M = 170 0 GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_21_208_24 163 test_chromosome 71 255 75M = 184 0 GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_22_173_62 99 test_chromosome 72 255 75M = 149 0 AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_23_186_42 163 test_chromosome 73 255 75M = 162 0 GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_26_189_30 163 test_chromosome 76 255 75M = 165 0 GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_28_188_11 99 test_chromosome 78 255 75M = 164 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_28_206_1f 73 test_chromosome 78 255 75M * 0 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_30_231_3c 161 test_chromosome 80 255 75M = 207 0 GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_33_189_4a 73 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_33_223_4e 73 test_chromosome 83 255 75M * 0 0 ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_36_146_27 163 test_chromosome 86 255 75M = 122 0 GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_36_218_12 99 test_chromosome 86 255 75M = 194 0 GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_38_199_29 99 test_chromosome 88 255 75M = 175 0 GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_39_219_5c 99 test_chromosome 89 255 75M = 195 0 CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_41_236_55 97 test_chromosome 91 255 75M = 212 0 AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_42_209_25 99 test_chromosome 92 255 75M = 185 0 GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_44_193_3f 99 test_chromosome 94 255 75M = 169 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_197_35 99 test_chromosome 94 255 75M = 173 0 ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_225_1e 163 test_chromosome 94 255 75M = 201 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_46_195_17 137 test_chromosome 96 255 75M * 0 0 GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_46_232_2f 99 test_chromosome 96 255 75M = 208 0 GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_207_39 73 test_chromosome 98 255 75M * 0 0 GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_48_249_20 161 test_chromosome 98 255 75M = 225 0 GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 163 test_chromosome 100 255 75M = 200 0 CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_51_194_47 163 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_51_194_49 99 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_51_237_a 99 test_chromosome 101 255 75M = 213 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_51_248_14 97 test_chromosome 101 255 75M = 224 0 ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_52_261_1b 97 test_chromosome 102 255 75M = 237 0 CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_53_212_19 99 test_chromosome 103 255 75M = 188 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_53_272_5a 161 test_chromosome 103 255 75M = 248 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_56_183_56 99 test_chromosome 106 255 75M = 159 0 GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_57_231_8 99 test_chromosome 107 255 75M = 207 0 GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 163 test_chromosome 108 255 75M = 194 0 GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_58_220_3d 163 test_chromosome 108 255 75M = 196 0 GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_58_234_7 163 test_chromosome 108 255 75M = 210 0 GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_63_229_4c 163 test_chromosome 113 255 75M = 205 0 ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 99 test_chromosome 115 255 75M = 214 0 GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_69_229_23 163 test_chromosome 119 255 75M = 205 0 AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 163 test_chromosome 122 255 75M = 234 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_73_240_34 99 test_chromosome 123 255 75M = 216 0 CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_259_5e 99 test_chromosome 123 255 75M = 235 0 CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_204_54 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_75_235_21 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_75_277_3b 97 test_chromosome 125 255 75M = 353 0 ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_77_256_2c 73 test_chromosome 127 255 75M * 0 0 GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_78_276_4b 97 test_chromosome 128 255 75M = 352 0 GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_79_256_31 137 test_chromosome 129 255 75M * 0 0 ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_81_228_3a 163 test_chromosome 131 255 75M = 204 0 GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_81_245_4d 163 test_chromosome 131 255 75M = 221 0 GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_82_255_2 137 test_chromosome 132 255 75M * 0 0 GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_82_271_58 99 test_chromosome 132 255 75M = 247 0 GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_85_268_53 99 test_chromosome 135 255 75M = 244 0 TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_85_275_38 137 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_87_250_57 163 test_chromosome 137 255 75M = 226 0 AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_87_279_5f 161 test_chromosome 137 255 75M = 355 0 AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_88_257_50 137 test_chromosome 138 255 75M * 0 0 GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_230_b 163 test_chromosome 139 255 75M = 206 0 AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_89_245_15 99 test_chromosome 139 255 75M = 221 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_89_267_32 163 test_chromosome 139 255 75M = 243 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_91_256_41 73 test_chromosome 141 255 75M * 0 0 CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_92_250_44 99 test_chromosome 142 255 75M = 226 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 -test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_92_266_43 99 test_chromosome 142 255 75M = 242 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_94_291_40 137 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_96_238_3 163 test_chromosome 146 255 75M = 214 0 GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_97_275_26 97 test_chromosome 147 255 75M = 351 0 ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_9_179_52 83 test_chromosome 155 255 75M = 59 0 ACTGGACCATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 Binary file test-data/tophat_out2.bam has changed

1 0

galaxy-dist commit 7ca26b1cc9b6: Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289194982 18000 # Node ID 7ca26b1cc9b6fd67364a6c6af6005ceecaa3f45b # Parent 535d276c92bcc35e563c4ce5a2351f562f451132 Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory. --- /dev/null +++ b/tool-data/all_fasta.loc.sample @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id><dbkey><display_name><file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# --- /dev/null +++ b/scripts/loc_files/create_all_fasta_loc.py @@ -0,0 +1,300 @@ +import optparse, os, sys +import elementtree.ElementTree as etree + +""" +Generates a loc file containing names of all the fasta files that match the +name of the genome subdirectory they're in. +Assumptions: + - fasta files should be named the same as the genome subdirectory they're + in, with the possible addition of a recognized variant (canon, full, etc.) + - for "variants" (like full, canon[ical], chrM, etc.) the naming needs to be + consistent and specific: + - <genome_name><variant>, like hg19canon, hg19full, or hg19chrM +Normal usage: +create_all_fasta_loc.py -f unmatching_fasta.txt -i seq + +usage: %prog [options] + -d, --data-table-xml=d: The name of the data table configuration file to get format of loc file + -t, --data-table=t: The name of the data table listed in the data table XML file + -g, --genome-dir=g: Genome directory to look in + -e, --exemptions=e: Comma-separated list of genome dir subdirectories to not look in + -i, --inspect-dirs=i: Comma-separated list of subdirectories inside genome dirs to look in (default is all) + -x, --fasta-exts=x: Comma-separated list of all fasta extensions to list + -s, --loc-sample=s: The name of the sample loc file (to copy text into top of output loc file) + -f, --unmatching-fasta=f: Name of file to output non-matching fasta files to, if included + -v, --variants=v: Comma-separated list of recognized variants of fasta file names + -a, --append=a: Append to existing all_fasta.loc file rather than create new + -p, --sample-text=p: Copy over text from all_fasta.loc.sample file (false if set to append) +""" + +DEFAULT_TOOL_DATA_TABLE_CONF = 'tool_data_table_conf.xml' +DEFAULT_ALL_FASTA_LOC_BASE = 'all_fasta' +DEFAULT_BASE_GENOME_DIR = '/afs/bx.psu.edu/depot/data/genome' +EXEMPTIONS = 'bin,tmp,lengths,equCab2_chrM,microbes' +INSPECT_DIR = None +FASTA_EXTS = '.fa,.fasta,.fna' +VARIANTS = 'chrM,chr21,full,canon,female,male,haps,nohaps' + +VARIANT_EXCLUSIONS = ':full' + +DBKEY_DESCRIPTION_MAP = { 'AaegL1': 'Mosquito (Aedes aegypti): AaegL1', + 'AgamP3': 'Mosquito (Anopheles gambiae): AgamP3', + 'anoCar1': 'Lizard (Anolis carolinensis): anoCar1', + 'anoGam1': 'Mosquito (Anopheles gambiae): anoGam1', + 'apiMel1': 'Honeybee (Apis mellifera): apiMel1', + 'apiMel2': 'Honeybee (Apis mellifera): apiMel2', + 'apiMel3': 'Honeybee (Apis mellifera): apiMel3', + 'Arabidopsis_thaliana_TAIR9': '', + 'borEut13': 'Boreoeutherian: borEut13', + 'bosTau2': 'Cow (Bos taurus): bosTau2', + 'bosTau3': 'Cow (Bos taurus): bosTau3', + 'bosTau4': 'Cow (Bos taurus): bosTau4', + 'bosTauMd3': 'Cow (Bos taurus): bosTauMd3', + 'calJac1': 'Marmoset (Callithrix jacchus): calJac1', + 'canFam1': 'Dog (Canis lupus familiaris): canFam1', + 'canFam2': 'Dog (Canis lupus familiaris): canFam2', + 'cavPor3': 'Guinea Pig (Cavia porcellus): cavPor3', + 'ce2': 'Caenorhabditis elegans: ce2', + 'ce4': 'Caenorhabditis elegans: ce4', + 'ce5': 'Caenorhabditis elegans: ce5', + 'ce6': 'Caenorhabditis elegans: ce6', + 'CpipJ1': 'Mosquito (Culex quinquefasciatus): CpipJ1', + 'danRer2': 'Zebrafish (Danio rerio): danRer2', + 'danRer3': 'Zebrafish (Danio rerio): danRer3', + 'danRer4': 'Zebrafish (Danio rerio): danRer4', + 'danRer5': 'Zebrafish (Danio rerio): danRer5', + 'danRer6': 'Zebrafish (Danio rerio): danRer6', + 'dm1': 'Fruit Fly (Drosophila melanogaster): dm1', + 'dm2': 'Fruit Fly (Drosophila melanogaster): dm2', + 'dm3': 'Fruit Fly (Drosophila melanogaster): dm3', + 'dm4': 'Fruit Fly (Drosophila melanogaster): dm', + 'dp3': 'Fruit Fly (Drosophila pseudoobscura): dp3', + 'dp4': 'Fruit Fly (Drosophila pseudoobscura): dp4', + 'droAna1': 'Fruit Fly (Drosophila ananassae): droAna1', + 'droAna2': 'Fruit Fly (Drosophila ananassae): droAna2', + 'droAna3': 'Fruit Fly (Drosophila ananassae): droAna3', + 'droEre1': 'Fruit Fly (Drosophila erecta): droEre1', + 'droEre2': 'Fruit Fly (Drosophila erecta): droEre2', + 'droGri1': 'Fruit Fly (Drosophila grimshawi): droGri1', + 'droGri2': 'Fruit Fly (Drosophila grimshawi): droGri2', + 'droMoj1': 'Fruit Fly (Drosophila mojavensis): droMoj1', + 'droMoj2': 'Fruit Fly (Drosophila mojavensis): droMoj2', + 'droMoj3': 'Fruit Fly (Drosophila mojavensis): droMoj3', + 'droPer1': 'Fruit Fly (Drosophila persimilis): droPer1', + 'droSec1': 'Fruit Fly (Drosophila sechellia): droSec1', + 'droSim1': 'Fruit Fly (Drosophila simulans): droSim1', + 'droVir1': 'Fruit Fly (Drosophila virilis): droVir1', + 'droVir2': 'Fruit Fly (Drosophila virilis): droVir2', + 'droVir3': 'Fruit Fly (Drosophila virilis): droVir3', + 'droYak1': 'Fruit Fly (Drosophila yakuba): droYak1', + 'droYak2': 'Fruit Fly (Drosophila yakuba): droYak2', + 'echTel1': 'Tenrec (Echinops telfairi): echTel1', + 'equCab1': 'Horse (Equus caballus): equCab1', + 'equCab2': 'Horse (Equus caballus): equCab2', + 'eriEur1': 'Hedgehog (Erinaceus europaeus): eriEur1', + 'felCat3': 'Cat (Felis catus): felCat3', + 'fr1': 'Fugu (Takifugu rubripes): fr1', + 'fr2': 'Fugu (Takifugu rubripes): fr2', + 'galGal2': 'Chicken (Gallus gallus): galGal2', + 'galGal3': 'Chicken (Gallus gallus): galGal3', + 'gasAcu1': 'Stickleback (Gasterosteus aculeatus): gasAcu1', + 'hg16': 'Human (Homo sapiens): hg16', + 'hg17': 'Human (Homo sapiens): hg17', + 'hg18': 'Human (Homo sapiens): hg18', + 'hg19': 'Human (Homo sapiens): hg19', + 'IscaW1': 'Deer Tick (Ixodes scapularis): IscaW1', + 'lMaj5': 'Leishmania major: lMaj5', + 'mm5': 'Mouse (Mus musculus): mm5', + 'mm6': 'Mouse (Mus musculus): mm6', + 'mm7': 'Mouse (Mus musculus): mm7', + 'mm8': 'Mouse (Mus musculus): mm8', + 'mm9': 'Mouse (Mus musculus): mm9', + 'monDom4': 'Opossum (Monodelphis domestica): monDom4', + 'monDom5': 'Opossum (Monodelphis domestica): monDom5', + 'ornAna1': 'Platypus (Ornithorhynchus anatinus): ornAna1', + 'oryCun1': 'Rabbit (Oryctolagus cuniculus): oryCun1', + 'oryLat1': 'Medaka (Oryzias latipes): oryLat1', + 'oryLat2': 'Medaka (Oryzias latipes): oryLat2', + 'oryza_sativa_japonica_nipponbare_IRGSP4.0': 'Rice (Oryza sativa L. ssp. japonica var. Nipponbare): IRGSP4.0', + 'otoGar1': 'Bushbaby (Otolemur garnetti): otoGar1', + 'panTro1': 'Chimpanzee (Pan troglodytes): panTro1', + 'panTro2': 'Chimpanzee (Pan troglodytes): panTro2', + 'petMar1': 'Lamprey (Petromyzon marinus): petMar1', + 'phiX': 'phiX174 (AF176034)', + 'PhumU1': 'Head Louse (Pediculus humanus): PhumU1', + 'ponAbe2': 'Orangutan (Pongo pygmaeus abelii): ponAbe2', + 'pUC18': 'pUC18 (L09136)', + 'rheMac2': 'Rhesus Macaque (Macaca mulatta): rheMac2', + 'rn3': 'Rat (Rattus norvegicus): rn3', + 'rn4': 'Rat (Rattus norvegicus): rn4', + 'sacCer1': 'Yeast (Saccharomyces cerevisiae): sacCer1', + 'sacCer2': 'Yeast (Saccharomyces cerevisiae): sacCer2', + 'sorAra1': 'Common Shrew (Sorex araneus): sorAra1', + 'Sscrofa9.58': 'Pig (Sus scrofa): Sscrofa9.58', + 'strPur2': 'Purple Sea Urchin (Strongylocentrotus purpuratus): strPur2', + 'susScr2': 'Pig (Sus scrofa): susScr2', + 'taeGut1': 'Zebra Finch (Taeniopygia guttata): taeGut1', + 'tetNig1': 'Tetraodon (Tetraodon nigroviridis): tetNig1', + 'tetNig2': 'Tetraodon (Tetraodon nigroviridis): tetNig2', + 'tupBel1': 'Tree Shrew (Tupaia belangeri): tupBel1', + 'venter1': 'Human (J. Craig Venter): venter1', + 'xenTro2': 'Frog (Xenopus tropicalis): xenTro2' + } + +VARIANT_MAP = { 'canon': 'Canonical', + 'full': 'Full', + 'female': 'Female', + 'male': 'Male' + } + +# alphabetize ignoring case +def caseless_compare( a, b ): + au = a.upper() + bu = b.upper() + if au > bu: + return 1 + elif au == bu: + return 0 + elif au < bu: + return -1 + +def __main__(): + # command line variables + parser = optparse.OptionParser() + parser.add_option( '-d', '--data-table-xml', dest='data_table_xml', type='string', default=DEFAULT_TOOL_DATA_TABLE_CONF, help='The name of the data table configuration file to get format of loc file' ) + parser.add_option( '-t', '--data-table', dest='data_table_name', type='string', default=DEFAULT_ALL_FASTA_LOC_BASE, help='The name of the data table listed in the data table XML file' ) + parser.add_option( '-g', '--genome_dir', dest='genome_dir', type='string', default=DEFAULT_BASE_GENOME_DIR, help='Genome directory to look in' ) + parser.add_option( '-e', '--exemptions', dest='exemptions', type='string', default=EXEMPTIONS, help='Comma-separated list of subdirectories in genome dir to not look in' ) + parser.add_option( '-i', '--inspect-dir', dest='inspect_dir', type='string', default=INSPECT_DIR, help='Comma-separated list of subdirectories inside genome dirs to look in (default is all)' ) + parser.add_option( '-x', '--fasta_exts', dest='fasta_exts', type='string', default=FASTA_EXTS, help='Comma-separated list of all fasta extensions to list' ) + parser.add_option( '-s', '--loc-sample', dest='loc_sample_name', type='string', help='The name of the sample loc file (to copy text into top of output loc file)' ) + parser.add_option( '-f', '--unmatching-fasta', dest='unmatching_fasta', type='string', default=None, help='Name of file to output non-matching fasta files to' ) + parser.add_option( '-v', '--variants', dest='variants', type='string', default=VARIANTS, help='Comma-separated list of recognized variants of fasta file names' ) + parser.add_option( '-n', '--variant-exclusions', dest='variant_exclusions', type='string', default=VARIANT_EXCLUSIONS, help="List of files to exclude because they're duplicated by a variants; of the format: '<variant_to_keep_1>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]][;<variant_to_keep_2>:<variant_to_remove_1>[,<variant_to_remove_2>[,...]]]'; default ':(full)' (if non-variant version present (like 'hg19'), full version (like 'hg19full') will be thrown out)" ) + parser.add_option( '-a', '--append', dest='append', action='store_true', default=False, help='Append to existing all_fasta.loc file rather than create new' ) + parser.add_option( '-p', '--sample-text', dest='sample_text', action='store_true', default='True', help='Copy over text from all_fasta.loc.sample file (false if set to append)' ) + (options, args) = parser.parse_args() + + exemptions = [ e.strip() for e in options.exemptions.split( ',' ) ] + fasta_exts = [ x.strip() for x in options.fasta_exts.split( ',' ) ] + variants = [ v.strip() for v in options.variants.split( ',' ) ] + variant_exclusions = {} + try: + for ve in options.variant_exclusions.split( ';' ): + v, e = ve.split( ':' ) + variant_exclusions[ v ] = e.split( ',' ) + except: + sys.stderr.write( 'Problem parsing the variant exclusion parameter (-n/--variant-exclusion). Make sure it follows the expected format\n' ) + sys.exit( 1 ) + if options.append: + sample_text = False + else: + sample_text = options.sample_text + + # all paths to look in + if options.inspect_dir: + paths_to_look_in = [ os.path.join( options.genome_dir, '%s', id ) for id in options.inspect_dir.split( ',' ) ] + else: + paths_to_look_in = os.path.join( options.genome_dir, '%s' ) + + # say what we're looking in + print '\nLooking in:\n\t%s' % '\n\t'.join( [ p % '<build_name>' for p in paths_to_look_in ] ) + poss_names = [ '<build_name>%s' % v for v in variants ] + print 'for files that are named %s' % ', '.join( poss_names[:-1] ), + if len( poss_names ) > 1: + print 'or %s' % poss_names[-1], + if len( options.fasta_exts ) == 1: + print 'with the extension %s.' % ', '.join( fasta_exts[:-1] ) + else: + print 'with the extension %s or %s.' % ( ', '.join( fasta_exts[:-1] ), fasta_exts[-1] ) + print '\nSkipping the following:\n\t%s' % '\n\t'.join( exemptions ) + + # get column names + col_values = [] + loc_path = None + tree = etree.parse( options.data_table_xml ) + tables = tree.getroot() + for table in tables.getiterator(): + name = table.attrib.get( 'name' ) + if name == options.data_table_name: + cols = None + for node in table.getiterator(): + if node.tag == 'columns': + cols = node.text + elif node.tag == 'file': + loc_path = node.attrib.get( 'path' ) + if cols: + col_values = [ col.strip() for col in cols.split( ',' ) ] + if not col_values or not loc_path: + stop_err( 'No columns can be found for this data table (%s) in %s' % ( options.data_table, options.data_table_xml ) ) + + # get all fasta paths under genome directory + fasta_locs = {} + unmatching_fasta_paths = [] + genome_subdirs = [ dr for dr in os.listdir( options.genome_dir ) if dr not in exemptions ] + for genome_subdir in genome_subdirs: + possible_names = [ genome_subdir ] + possible_names.extend( [ '%s%s' % ( genome_subdir, v ) for v in variants ] ) + # get paths to all fasta files + for path_to_look_in in paths_to_look_in: + for dirpath, dirnames, filenames in os.walk( path_to_look_in % genome_subdir ): + for fn in filenames: + ext = os.path.splitext( fn )[-1] + fasta_base = os.path.splitext( fn )[0] + if ext in fasta_exts: + if fasta_base in possible_names: + if fasta_base == genome_subdir: + name = DBKEY_DESCRIPTION_MAP[ genome_subdir ] + else: + try: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], VARIANT_MAP[ fasta_base.replace( genome_subdir, '' ) ] ) + except KeyError: + name = '%s %s' % ( DBKEY_DESCRIPTION_MAP[ genome_subdir ], fasta_base.replace( genome_subdir, '' ) ) + fasta_locs[ fasta_base ] = { 'value': fasta_base, 'dbkey': genome_subdir, 'name': name, 'path': os.path.join( dirpath, fn ) } + else: + unmatching_fasta_paths.append( os.path.join( dirpath, fn ) ) + # remove redundant fasta files + if variant_exclusions.keys(): + for k in variant_exclusions.keys(): + leave_in = '%s%s' % ( genome_subdir, k ) + if fasta_locs.has_key( leave_in ): + to_remove = [ '%s%s' % ( genome_subdir, k ) for k in variant_exclusions[ k ] ] + for tr in to_remove: + if fasta_locs.has_key( tr ): + del fasta_locs[ tr ] + + # output results + print '\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len( unmatching_fasta_paths ) + print '%s fasta files were found and listed.\n' % len( fasta_locs.keys() ) + + # output unmatching fasta files + if options.unmatching_fasta and unmatching_fasta_paths: + open( options.unmatching_fasta, 'wb' ).write( '%s\n' % '\n'.join( unmatching_fasta_paths ) ) + + # output loc file + if options.append: + all_fasta_loc = open( loc_path, 'ab' ) + else: + all_fasta_loc = open( loc_path, 'wb' ) + # put sample loc file text at top of file if appropriate + if sample_text: + if options.loc_sample_name: + all_fasta_loc.write( '%s\n' % open( options.loc_sample_name, 'rb' ).read().strip() ) + else: + all_fasta_loc.write( '%s\n' % open( '%s.sample' % loc_path, 'rb' ).read().strip() ) + # output list of fasta files in alphabetical order + fasta_bases = fasta_locs.keys() + fasta_bases.sort( caseless_compare ) + for fb in fasta_bases: + out_line = [] + for col in col_values: + try: + out_line.append( fasta_locs[ fb ][ col ] ) + except KeyError: + stop_err( 'Unexpected column (%s) encountered' % col ) + if out_line: + all_fasta_loc.write( '%s\n' % '\t'.join( out_line ) ) + # close up output loc file + all_fasta_loc.close() + +if __name__=='__main__': __main__()

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galaxy-dist commit 535d276c92bc: Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1289193013 18000 # Node ID 535d276c92bcc35e563c4ce5a2351f562f451132 # Parent 4187ae2fdb9e3f8b7ff5878e7517a24868b8ffca Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters. --- a/test-data/bwa_wrapper_out1.sam +++ b/test-data/bwa_wrapper_out1.sam @@ -1,30 +1,30 @@ -seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 -seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 -seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII -seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 -seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 -seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 -seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 -seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 --- a/test-data/perm_in2.fastqsanger +++ b/test-data/perm_in2.fastqsanger @@ -1,76 +1,76 @@ @HWI-EAS91_1_30788AAXX:1:1:1761:343/2 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG -+/2 ++ IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1578:331/2 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1647:512/2 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1570:620/2 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1599:330/2 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1652:270/2 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1746:351/2 CCACTCCTCTCCCGACTGTGTGTGTGTGTGTTTATATTGACCATGCCGCT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIII?I0IIIIHIIIGIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1582:633/2 TCTATTGACATTATGGGTCTGCAAGCTGCTTTTTTTTTTTTTTTTTTTTT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1598:534/2 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1572:324/2 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1749:466/2 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1629:446/2 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1763:587/2 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1616:363/2 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1768:715/2 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA -+/2 ++ IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1572:270/2 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1785:1272/2 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC -+/2 ++ III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1673:514/2 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII @HWI-EAS91_1_30788AAXX:1:1:1634:330/2 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTAT -+/2 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -1,49 +1,55 @@ -<tool id="PerM" name="Map with PerM" version="1.0.0"> +<tool id="PerM" name="Map with PerM" version="1.1.0"><description>for SOLiD and Illumina</description><requirements><requirement type="package">perm</requirement></requirements><command> -PerM -#if $s.sourceOfRef.refSource == "history": - $s.sourceOfRef.ref -#else: - $s.sourceOfRef.index -#end if -#if $s.mate.singleOrPairs == "single": - $s.mate.reads -#else: - -1 $s.mate.reads1 -2 $s.mate.reads2 - -U $s.mate.upperbound - -L $s.mate.lowerbound - $s.mate.excludeAmbiguousPairs -#end if -#if $s.space == "color": - --readFormat "csfastq" -#else: - --readFormat "fastq" -#end if -#if $int($str($valAlign)) >= 0: - -v $valAlign -#end if -#if $align.options == "full": - --seed $align.seed - -$align.alignments - #if $str($align.delimiter) != "None": - --delimiter $align.delimiter - #end if - -T $align.sTrimL - $align.includeReadsWN - $align.statsOnly - $align.ignoreQS -#end if -#if $str($bUnmappedRead) == "true" and $s.space == "color": - -u $unmappedReadOutCS -#elif $str($bUnmappedRead) == "true" and $s.space == "base": - -u $unmappedReadOut -#end if --o $output --outputFormat sam --noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/' + PerM + #if $s.sourceOfRef.refSource == "history" + $s.sourceOfRef.ref + #else + #if $s.space == "color" + "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + #elif $s.space == "base" + "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + #end if + #end if + #if $s.mate.singleOrPairs == "single": + $s.mate.reads + #else: + -1 $s.mate.reads1 -2 $s.mate.reads2 + -U $s.mate.upperbound + -L $s.mate.lowerbound + $s.mate.excludeAmbiguousPairs + #end if + #if $s.space == "color": + --readFormat "csfastq" + #else: + --readFormat "fastq" + #end if + #if $int($str($valAlign)) >= 0 + -v $valAlign + #end if + #if $align.options == "full": + --seed $align.seed + -$align.alignments + #if $str($align.delimiter) != "None" + --delimiter $align.delimiter + #end if + -T $align.sTrimL + $align.includeReadsWN + $align.statsOnly + $align.ignoreQS + #end if + #if $str($bUnmappedRead) == "true" and $s.space == "color" + -u $unmappedReadOutCS + #elif $str($bUnmappedRead) == "true" and $s.space == "base" + -u $unmappedReadOut + #end if + -o $output + --outputFormat sam + --noSamHeader | tr '\r' '\n' | tr -cd "[:print:]\t\n " | grep "Reads\|Sub0\|Pairs\|single" | sed 's/.*Reads:,//' | sed 's/\/.*dat,_ Sub0/Sub0/' </command><inputs><conditional name="s"> @@ -59,10 +65,7 @@ PerM </param><when value="indexed"><param name="index" type="select" label="Select a reference genome (with seed and read length)" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="perm_color_index.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="perm_color_indexes"/></param></when><when value="history"> @@ -94,10 +97,7 @@ PerM </param><when value="indexed"><param name="index" type="select" label="Select a reference genome with seed and read length" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="perm_base_index.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="perm_base_indexes"/></param></when><when value="history"> @@ -148,7 +148,7 @@ PerM </param><param label="Use the first n bases of each read for alignment (-T)" name="sTrimL" type="integer" size="5" value="50" /><param name="includeReadsWN" type="boolean" checked="true" truevalue="--includeReadsWN" falsevalue="" label="Include reads with 'N' or '.' by encoding '.' as 3, 'N' as 'A' (--includeReadsWN)" /> - <param name="statsOnly" type="boolean" checked="false" truevalue="--statsOnly" falsevalue="" label="output mapping stats only. Don't output alignments (--statsOnly)" /> + <param name="statsOnly" type="boolean" checked="false" truevalue="--statsOnly" falsevalue="" label="Output mapping stats only. Don't output alignments (--statsOnly)" /><param name="ignoreQS" type="boolean" checked="false" truevalue="--ignoreQS" falsevalue="" label="Ignore quality scores (--ignoreQS)" /></when></conditional> @@ -170,8 +170,7 @@ PerM <test><param name="space" value="base" /> @@ -186,7 +185,7 @@ PerM <param name="valAlign" value="0" /><param name="options" value="full" /><param name="alignments" value="A" /> - <param name="seed" value="F2" /> + <param name="seed" value="F3" /><param name="delimiter" value="None" /><param name="sTrimL" value="50" /><param name="includeReadsWN" value="true" /> @@ -198,7 +197,7 @@ PerM <test><param name="space" value="base" /> @@ -215,7 +214,7 @@ PerM <test><param name="space" value="color" /> @@ -231,14 +230,12 @@ PerM <test><param name="space" value="color" /><param name="refSource" value="indexed" /> - <param name="index" value="equCab2_chrM_F3_50" /> + <param name="index" value="equCab2_chrM_F2_50" /><param name="singleOrPairs" value="paired" /><param name="reads1" value="perm_in5.fastqcssanger" ftype="fastqcssanger" /><param name="reads2" value="perm_in6.fastqcssanger" ftype="fastqcssanger" /> --- a/test-data/perm_in3.fastqsanger +++ b/test-data/perm_in3.fastqsanger @@ -1,396 +1,396 @@ @HWI-EAS91_1_30788AAXX:1:1:1513:715/1 GTTTTTTGGGCATAGATGTTTAGTTGTGGTAGTCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I @HWI-EAS91_1_30788AAXX:1:1:1698:516/1 GTTGTTAGGGAGAGGAGTTGAACCTCTGAGTGTAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIII5IIIII9I @HWI-EAS91_1_30788AAXX:1:1:1491:637/1 GCTAGCAGGATGGATCCGGCAATTGGGGCTTCTACA -+/1 ++ IIIIIII""IIIIIIIIIIIIFIIIIIIIIIIIABD @HWI-EAS91_1_30788AAXX:1:1:1711:249/1 GGAAGTAGGGGCCTGCGTTCAGGCGTTCTGTTTGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1634:211/1 GAAGCAGGGGCTTGATACTGACACTTCGTCGACGTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF @HWI-EAS91_1_30788AAXX:1:1:1218:141/1 GTTAAATATTGGGAGTGGGGGGGGGGGGGAGTTTTGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII1IIII+I @HWI-EAS91_1_30788AAXX:1:1:1398:854/1 GTGAAGAGGAGGGGATTTATTAGTACGGGAAGGGTG -+/1 ++ IIIIIII""IIIIIBIIIIIIIIIIIIIIA=IIIII @HWI-EAS91_1_30788AAXX:1:1:1310:991/1 GAATAGTGGTAGTATTATTCCTTCTAGGCATAGGAG -+/1 ++ IIIIIII""IIIIIIIIII4IIIIIIDII:IEI2:I @HWI-EAS91_1_30788AAXX:1:1:1716:413/1 GATCCAAGGCTTTATCAACACCTATTCTGATTCTTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1630:59/1 GGAGCGGGGGGTTGGTAAGGTTGGGGTCGAGTATGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII;IIHIIF @HWI-EAS91_1_30788AAXX:1:1:1601:805/1 GAAAACAGGAAAACAATCCAGTCACTTACCCTATGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII@III @HWI-EAS91_1_30788AAXX:1:1:1663:724/1 GTTTGCCGGCGCCATCCTACGCTCCATTCCCAACAA -+/1 ++ IIIIIII""IIII8IIIIIIHIIII6IIIII1CI=3 @HWI-EAS91_1_30788AAXX:1:1:1454:975/1 GCTAGGCGGGAGTGGTAAAAGGCTCAGAAGAAGCCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIEIG;IIIIIII @HWI-EAS91_1_30788AAXX:1:1:1461:255/1 GTACACCGGCGCCTGAGCCCTACTAATAACTCTCAT -+/1 ++ IIIIIII""IIIIII9IIIIIIEI(II9.I4III,I @HWI-EAS91_1_30788AAXX:1:1:1775:764/1 GCATCCCGGTAGATCTAATTTTCTAAATCTGTCAAC -+/1 ++ IIIIIII""III@IIII+IIIIII8H8IIIIIIICI @HWI-EAS91_1_30788AAXX:1:1:1269:520/1 GGAGTATGGAATAAGTGATTTTAGATCGGTTTGTCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1303:1162/1 GAGCAAGGGCAGGAGGAGGAGTCCTAGGATGTCTTT -+/1 ++ IIIIIII""IIIIFII4*IGIAI(IAII49',3I6I @HWI-EAS91_1_30788AAXX:1:1:1090:409/1 GTTTGTTGGGAATGGAGCGTAGGATGGCGTAGGCAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII:IIA8I @HWI-EAS91_1_30788AAXX:1:1:1336:1000/1 GGTAAATGGGAAATATTAAGTTTCTGTTTCTAGATC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII9II @HWI-EAS91_1_30788AAXX:1:1:1199:1376/1 GTTTTCTGGAAAACCTTCACCTATTTATGGGGGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIII;III3IIG&:/III @HWI-EAS91_1_30788AAXX:1:1:1598:1148/1 GATCAATGGTTTGGATCAATAAGTGATTATATATTT -+/1 ++ IIIIIII""IIIIIDIIIIII?IIICII=IHIIIII @HWI-EAS91_1_30788AAXX:1:1:1723:1459/1 GAAACCCGGACGTTTGGATGGGCCCGGAGCGAGGAT -+/1 ++ IIIIIII""IIIIIIIIDIIIIIIIII9HII-II=I @HWI-EAS91_1_30788AAXX:1:1:1442:1346/1 TATCAAGGGGCTGCTTCGAATCCGAAGTGGTGGCTG -+/1 ++ IIIIIII""IIIIIDIIIII1I(I4II<?<-II*,& @HWI-EAS91_1_30788AAXX:1:1:850:117/1 GTATGACGGTAAAGAAAATTATTACGAATGCATGGG -+/1 ++ IIIIIII""IIIIIIEIEIIIIIIIIEBIDD9I;:? @HWI-EAS91_1_30788AAXX:1:1:795:325/1 GGGTACTGGGAAGTGGAATGGTGTGAGTCCAAGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII65IIII @HWI-EAS91_1_30788AAXX:1:1:873:453/1 GAGTAGGGGGATTGCTAGAGTTACTTCGTATGAGAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII@IIIIIII=I @HWI-EAS91_1_30788AAXX:1:1:1285:1334/1 GATATGGGGTCTGGAATAGGATTGCGCTGTTATCCC -+/1 ++ IIIIIII""IIIIIBIIGIIIIIIIIII8IIIII8I @HWI-EAS91_1_30788AAXX:1:1:905:406/1 GAAAAGTGGTAGGCTATATGCAACTTCGCAAAGGAC -+/1 ++ IIIIIII""IIIIIIIIBIIIIBIIII=I@96D2*I @HWI-EAS91_1_30788AAXX:1:1:1774:595/1 TTTAGGTGGGATGTGGGGATCATGTAGGAGTCAAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIEI @HWI-EAS91_1_30788AAXX:1:1:1694:931/1 TTAAATTGGCATTAGAATTGAGTAGTTTTTAGGTAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIH,III @HWI-EAS91_1_30788AAXX:1:1:1092:1151/1 GAGAGTTGGCTGATTTAGGCGCCCAGGGATAGCGTC -+/1 ++ IIIIIII""IIIIIIIIIII5III>IIIII6@III5 @HWI-EAS91_1_30788AAXX:1:1:803:557/1 GGTGTGTGGGCGCTTCATGGCCTGATTCAATTAAGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIII<IIII?III406 @HWI-EAS91_1_30788AAXX:1:1:1315:1200/1 TAGTTTTGGGGGGTTTTCTTCAAAACCTTCACCTAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII;I @HWI-EAS91_1_30788AAXX:1:1:765:358/1 GGTGTTTGGATGAGGACGGCTACGATTACTAGGGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIDIIAII4@I0D='1I @HWI-EAS91_1_30788AAXX:1:1:1425:1167/1 GACCTTAGGTGTAGGACATGGTGTAATTCGGTAGCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII(%II+IG @HWI-EAS91_1_30788AAXX:1:1:1775:635/1 AATAGCCGGATAGCTAGAAGTAAGGTTGAGTTAAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIBI @HWI-EAS91_1_30788AAXX:1:1:1433:749/1 GACTATGGGTGCTATTATACATGCTAGTCATAGGAA -+/1 ++ IIIIIII""IIIIIIIIIIIFIIIIICIIIIB/I9E @HWI-EAS91_1_30788AAXX:1:1:798:247/1 GGAGATTGGAAAGTAGTATGCTTAGGGTAAGGGTGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1249:1238/1 TATTGTTGGGGTAGCGAAAGAGGCGAATAGATTTTC -+/1 ++ IIIIIII""IIIIIIIIIIIBIIIICDIII7IIII@ @HWI-EAS91_1_30788AAXX:1:1:1043:1104/1 GGAAGGGGGAATAGGAGGGCAATTTCTAAGTCGAAT -+/1 ++ II&IIII""IIIIIIDIIIII;IFI<I0II.IIIC, @HWI-EAS91_1_30788AAXX:1:1:1655:1058/1 AAAAATCGGCTTTACAATTATATTCGTAGGGGTAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIFIII6AIIIGI @HWI-EAS91_1_30788AAXX:1:1:1764:1403/1 TGATGAAGGGTTTGAGGGGGCTGGTAGGTCAATAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIBIIIII @HWI-EAS91_1_30788AAXX:1:1:1632:34/1 AGGATAGGGGCTATCCGTTGGTCTTAGGAACCAAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIFIIIH:6I @HWI-EAS91_1_30788AAXX:1:1:1367:1208/1 GACACGTGGCACTTCCAATCATACTATCCAGCATCC -+/1 ++ IIIIIII""IIIIIIII:IIII8IIEIIII-IAIII @HWI-EAS91_1_30788AAXX:1:1:1778:108/1 AATACACGGACCATATCAACAGCATTAAACCTTCAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII@I @HWI-EAS91_1_30788AAXX:1:1:1152:1115/1 GTAGTATGGCGTAGCCTCCTAGTTTTAGTAGAATGG -+/1 ++ 7IIIIII""IIIIIIIIIII.68IIIDII=7IIIA' @HWI-EAS91_1_30788AAXX:1:1:1165:1121/1 ATACTCAGGTCATTCTAGTCCTTTTTGGGTTCATTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII22?IIIIIIA @HWI-EAS91_1_30788AAXX:1:1:1500:55/1 ATAGAGAGGAGTGCAACTAAGAGTGGGAGGGAACCT -+/1 ++ IIIIIII""IIIIIIIIIIFIIIIIIICIII<IIII @HWI-EAS91_1_30788AAXX:1:1:1142:1196/1 TCATTTTGGTACCACTCGCAAGCACCATCGAAAACA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII@I=I79I6II @HWI-EAS91_1_30788AAXX:1:1:1693:757/1 AAATTATGGGTTAAACCCCTATATACCTCTATGGCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIBIDIIIII0II-IG @HWI-EAS91_1_30788AAXX:1:1:1364:1053/1 TTATTCAGGTGGGTATGAATCCTGATAGTGGGGGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIII?.I31G&4=5 @HWI-EAS91_1_30788AAXX:1:1:1450:1443/1 GTAAAAAGGTGCTCCAAGGCCTATTCATCACAATTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIEIB8III @HWI-EAS91_1_30788AAXX:1:1:1701:1298/1 TAGTAGAGGCCGCGTCCTACGTGAATGAAGAGGCAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII8II;IIIGI @HWI-EAS91_1_30788AAXX:1:1:1729:856/1 TCCTATTGGTTCAATACTGAAACCAAGCACTACCCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIFIIIII@IIIH @HWI-EAS91_1_30788AAXX:1:1:1748:933/1 TGAGCTCGGGGCTTCATCTTCTTATTCACAGTAGGA -+/1 ++ IIIIIII""IIIIIICIIIIIIIIIIIIII@II5@F @HWI-EAS91_1_30788AAXX:1:1:1662:1296/1 TTAGTTAGGAATAGAATTACACATGCAAGTATCCGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIHIIIEI5IIIII4I @HWI-EAS91_1_30788AAXX:1:1:1393:345/1 ATTTACAGGAGAATTGAGTAGTTTTTAGGTAAATTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIE+IIEIIII @HWI-EAS91_1_30788AAXX:1:1:943:780/1 AGGCGTTGGGTTTGGTTGCCTCAGCGGGTGATGATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII;II<IH @HWI-EAS91_1_30788AAXX:1:1:1639:968/1 AGCTCACGGAAAATAGCAGCATCATCCTCCCCACAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8I:I @HWI-EAS91_1_30788AAXX:1:1:589:1114/1 GTCATTCGGGATTAGTTGAGGTTAATTCTACTGTAG -+/1 ++ IIIIIII""IIIIIIIIIII1IIIIIIIIIII&II) @HWI-EAS91_1_30788AAXX:1:1:763:408/1 GCCCCACGGCTGGTGTTGACAACATGACTACTGCCA -+/1 ++ IIIIIII""IIIIIIIIIIIIII=I*5II<II'II( @HWI-EAS91_1_30788AAXX:1:1:950:352/1 ACGCATAGGCAACATGAAATACCATCTCATCCATAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIFIIIIIGI @HWI-EAS91_1_30788AAXX:1:1:1164:103/1 TTAACTAGGACATTCACCAAACCATTAAAGTATAGG -+/1 ++ IIIIIII""IIIIIIIIIIIAII=IIB58I=<I;II @HWI-EAS91_1_30788AAXX:1:1:1078:1202/1 TAGGGCTGGGCATAGTGGGGTATCTAATCCCAGTTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIEIII @HWI-EAS91_1_30788AAXX:1:1:1617:490/1 AATCCTTGGTAACCGCATCGGGGATATCGGCTTCAT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIII:(D @HWI-EAS91_1_30788AAXX:1:1:843:504/1 ACAACATGGAATACCATCTCATCCATAGGATCTTTT -+/1 ++ IIIIIII""IIIIIIIIAIIIIII>IIHI=IIIIII @HWI-EAS91_1_30788AAXX:1:1:942:318/1 TTCATACGGGCCATGTCCAGCCTAGCTGTCTACTCA -+/1 ++ IIIIIII""IIIIIIIIIIHIIIIIIIIIII<IIIF @HWI-EAS91_1_30788AAXX:1:1:1719:283/1 TTTTGTTGGCCGAGGTCACCCCAACCGAAATTGCTG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII3=2IGIIII @HWI-EAS91_1_30788AAXX:1:1:1517:961/1 TGTCACTGGTCCATATTAATATCTTCCTAGCATTCA -+/1 ++ IIIIIII""IIIII=III9I@IIIIIIIBIIEIII> @HWI-EAS91_1_30788AAXX:1:1:1482:345/1 AGGATGTGGGTTAATAGCCCTATAGCTAGAAGTAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?IAHIIAAI @HWI-EAS91_1_30788AAXX:1:1:1697:533/1 ATGAGGTGGATTAGGAGGTGTCCGGCGGTAATGTTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII1>IIIII @HWI-EAS91_1_30788AAXX:1:1:1159:1225/1 TTTCTACGGCAAGGGACGCCCATTTTCCTCATCCCC -+/1 ++ IIIIIII""IIIII=I7IIII3IIIIIIII/ID@II @HWI-EAS91_1_30788AAXX:1:1:982:332/1 AAGGATTGGATCCCCTCCTCCTGCGGGGTCGAAGAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIII?<I7@ @HWI-EAS91_1_30788AAXX:1:1:1073:668/1 AGCATTTGGCAACCCCTACCTGCCAGAACTCTACTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIII>I4@IIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1386:1163/1 AGTTGGCGGAAAAGCAGCCATCAATTAAGAAAGCGT -+/1 ++ IIIIIII""IIIIIIIIIICII=GIIIII@IGIIII @HWI-EAS91_1_30788AAXX:1:1:1196:344/1 ATTGAAGGGAGTTGATTAGGGTATTTAGCTGTTAAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII7 @HWI-EAS91_1_30788AAXX:1:1:1551:1269/1 ATTACCAGGATCCTAATAGGAGCCAATATCACCATC -+/1 ++ IIIIIII""IIIIIIIIGIIIIIIIIIIII@II4II @HWI-EAS91_1_30788AAXX:1:1:928:468/1 AGGAGATGGAAATTTTAACTTGGCGCTATAGAGAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIC<IHIII @HWI-EAS91_1_30788AAXX:1:1:763:835/1 GCTCAGAGGAAGCCAGAGAAGAAGAAGACTTCTGAG -+/1 ++ IIIIIII""IIIIIIIHIEFIIFI<IIIIIIDII:I @HWI-EAS91_1_30788AAXX:1:1:1363:330/1 TAGCCTCGGAGTTTTAGTAGAATGGCTGCTAGCACT -+/1 ++ IIIIIII""IIIIIIII@IIIIIIIIII5I,5C-75 @HWI-EAS91_1_30788AAXX:1:1:1001:837/1 ATACTATGGCTGTGAGGAATAATCATAACTAGTTCC -+/1 ++ IIIIIII""IIIII2IIIIIIIIIIIFIII:IIIII @HWI-EAS91_1_30788AAXX:1:1:1189:616/1 TTTGATAGGGTAAAACATAGAGGCTCAAACCCTCTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIICIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1212:634/1 ATCAACAGGTATTCTGATTCTTCGGACACCCCGAAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIAIIIIF(.I @HWI-EAS91_1_30788AAXX:1:1:1271:421/1 ACACGACGGCACCTAATGACCCACCAAACCCACGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIII>C:IIIDI<II @HWI-EAS91_1_30788AAXX:1:1:1582:328/1 AGCATTAGGCTTTTAAGTTAAAGATTGAGGGTTCAA -+/1 ++ IIIIIII""IIIIII,IIIB;BI<IIIIII+IIIBI @HWI-EAS91_1_30788AAXX:1:1:1133:687/1 AGAGAGCGGATTAGGAATACGATTATTAGTGTGTGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII4III @HWI-EAS91_1_30788AAXX:1:1:1231:662/1 TCACTCTGGAGAACATATAAAACCAACATAACCTCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?ICCIIIII @HWI-EAS91_1_30788AAXX:1:1:1693:1140/1 ATTGATAGGATGGGGGTTAGGGGGAGGAGTAGGGAG -+/1 ++ IIIIIII""IIIIIIIIIIIIIII:II5II7IIA-I @HWI-EAS91_1_30788AAXX:1:1:867:279/1 AAGCATTGGACTGTAAATCTAAAGACAGGGGTTGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1095:605/1 AAGCAAGGGACTGAAAATGCCTAGATGAGTATTCTT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1650:1185/1 ACCCCAGGGAACCCTCTCAGCACTCCCCCTCATATT -+/1 ++ IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II @HWI-EAS91_1_30788AAXX:1:1:799:192/1 AATGTTAGGGGTTAGCCGCACGGCTAGGGCTACAGG -+/1 ++ IIIIIII""IIIIIIIIII8IIIEIIIII<I::%II @HWI-EAS91_1_30788AAXX:1:1:1082:719/1 TCTTGAGGGTCTATGGTGCTGGTATGGGTTAATTTA -+/1 ++ IIIIIII""IIIIIIA8III>I92I3+3IIE0III< @HWI-EAS91_1_30788AAXX:1:1:1746:1180/1 AAAATTAGGGAGAAGTAATCTAGTTTGAAGCTTAGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIFIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:606:460/1 TTAATTTGGATTATAATAACACTCACAATATTCATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 @HWI-EAS91_1_30788AAXX:1:1:1059:362/1 ATCGGTAGGCTCGTAGCTTCAGTATCATTGGTGGCC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIII2)</II @HWI-EAS91_1_30788AAXX:1:1:1483:1161/1 ATATGTGGGGGGTGGGGATGAGTGCTAGGATCAGGA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIHIAIIFIIIIIH @HWI-EAS91_1_30788AAXX:1:1:1273:600/1 TACTGAGGGGTATCCTGAGGTATGGGTGTCTAATAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII @HWI-EAS91_1_30788AAXX:1:1:1190:1283/1 TTTCTGGGGTACAAGACCAGGGTAATGTGCGATATA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIAIIIII-?IIIE --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -1,25 +1,42 @@ -<tool id="lastz_wrapper_2" name="Lastz" version="1.1.1"> +<tool id="lastz_wrapper_2" name="Lastz" version="1.2.0"><description> map short reads against reference sequence</description><command interpreter="python">lastz_wrapper.py -#if $seq_name.how_to_name=="yes": ---ref_name=$seq_name.ref_name -#else: ---ref_name="None" -#end if ---ref_source=$source.ref_source --source_select=$params.source_select --out_format=$out_format --input2=$input2 -#if $source.ref_source=="history": ---input1=$source.input1 ---ref_sequences=$input1.metadata.sequences -#else: ---input1=$source.input1_2bit ---ref_sequences="None" -#end if -#if $params.source_select=="pre_set": ---pre_set_options=${params.pre_set_options} --strand="None" --seed="None" --gfextend="None" --chain="None" --transition="None" --O="None" --E="None" --X="None" --Y="None" --K="None" --L="None" --entropy="None" -#else: ---pre_set_options="None" --strand=$params.strand --seed=$params.seed --gfextend=$params.gfextend --chain=$params.chain --transition="$params.transition" --O=$params.O --E=$params.E --X=$params.X --Y=$params.Y --K=$params.K --L=$params.L --entropy=$params.entropy -#end if ---identity_min=$min_ident --identity_max=$max_ident --coverage=$min_cvrg --output=$output1 --unmask=$unmask --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} + #if $seq_name.how_to_name=="yes": + --ref_name=$seq_name.ref_name + #end if + --ref_source=$source.ref_source + --source_select=$params.source_select + --out_format=$out_format + --input2=$input2 + #if $source.ref_source=="history": + --input1=$source.input1 + --ref_sequences=$input1.metadata.sequences + #else: + --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --ref_sequences="None" + #end if + #if $params.source_select=="pre_set": + --pre_set_options=${params.pre_set_options} + #else: + --strand=$params.strand + --seed=$params.seed + --gfextend=$params.gfextend + --chain=$params.chain + --transition="$params.transition" + --O=$params.O + --E=$params.E + --X=$params.X + --Y=$params.Y + --K=$params.K + --L=$params.L + --entropy=$params.entropy + #end if + --identity_min=$min_ident + --identity_max=$max_ident + --coverage=$min_cvrg + --output=$output1 + --unmask=$unmask + --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} </command><inputs><param name="input2" format="fasta" type="data" label="Align sequencing reads in" /> @@ -30,10 +47,7 @@ </param><when value="cached"><param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="lastz_seqs.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="lastz_seqs" /></param></when><when value="history"> @@ -127,14 +141,15 @@ <tests><test> - <param name="input2" value="b1.fasta" ftype="fasta" /> + <param name="input2" value="b1.fasta" ftype="fasta" dbkey="phiX" /><param name="ref_source" value="cached" /> - <param name="input1_2bit" value="phiX" /> +  + <param name="input1_2bit" value="/galaxy/data/phiX/seq/phiX.2bit" /><param name="out_format" value="sam" /><param name="source_select" value="full" /><param name="strand" value="both" /> @@ -150,8 +165,8 @@ <param name="L" value="3000" /><param name="entropy" value="noentropy" /><param name="how_to_name" value="yes" /><param name="ref_name" value="Ref" /> @@ -163,10 +178,10 @@ </test><test><param name="input2" value="b1.fasta" ftype="fasta" /><param name="ref_source" value="history" /> @@ -183,17 +198,17 @@ </test><test><param name="input2" value="b1.fasta" ftype="fasta" /><param name="ref_source" value="history" /> --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -1,12 +1,27 @@ #This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using two columns tab separated: +#list of protein BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): # -#<database caption><path to base name> +#<unique_id><database_caption><base_name_path> # -#For example: +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that the first tab that appears in the line is right before the path. # -#NCBI NR (non redundant) /data/blastdb/nr +#So, for example, if your database is NR and the path to your base name +#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#where /data/blastdb/nr.* are the files making up the NR database. +#nr NCBI NR (non redundant) /data/blastdb/nr # -#See also the blastdb.loc file which is for any nucleotide databases. +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/nr.*. +# +#Your blastdb_p.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#...etc... +# +#See also blastdb.loc which is for any nucleotide BLAST database. +# --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -3,9 +3,9 @@ #to create these data files and then create a perm_base_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The perm_base_index.loc -#file has this format (white space characters are TAB characters): +#file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,8 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_base_F3_50.index +# --- a/test-data/lastz_wrapper_out2.sam +++ b/test-data/lastz_wrapper_out2.sam @@ -1,459 +1,459 @@ -HWI-EAS91_1_306UPAAXX 16 PHIX174 4295 255 1H35M * 0 0 CCCCCAACTTGATATTAATAACACTATAGACCACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3522 255 36M * 0 0 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 229 255 36M * 0 0 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1067 255 1H35M * 0 0 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1788 255 36M * 0 0 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4563 255 36M * 0 0 GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2668 255 36M * 0 0 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4248 255 36M * 0 0 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2511 255 34M2H * 0 0 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5152 255 36M * 0 0 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4884 255 36M * 0 0 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5052 255 36M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4909 255 36M * 0 0 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4173 255 36M * 0 0 GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1701 255 36M * 0 0 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1683 255 36M * 0 0 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3126 255 1H35M * 0 0 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1665 255 36M * 0 0 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3213 255 36M * 0 0 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3420 255 36M * 0 0 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 513 255 36M * 0 0 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2879 255 36M * 0 0 ATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4471 255 36M * 0 0 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1229 255 36M * 0 0 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 615 255 36M * 0 0 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 257 255 36M * 0 0 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2381 255 36M * 0 0 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4098 255 36M * 0 0 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5099 255 36M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3408 255 36M * 0 0 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4043 255 36M * 0 0 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4560 255 36M * 0 0 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1888 255 36M * 0 0 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3434 255 1H35M * 0 0 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4539 255 36M * 0 0 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1828 255 36M * 0 0 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3708 255 36M * 0 0 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3326 255 36M * 0 0 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4176 255 36M * 0 0 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 22 255 36M * 0 0 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3277 255 36M * 0 0 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3592 255 36M * 0 0 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 358 255 35M1H * 0 0 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1775 255 36M * 0 0 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3504 255 36M * 0 0 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1554 255 36M * 0 0 CGACTTCTACCACATCTATTGACATTATGGGTCTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3626 255 36M * 0 0 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3572 255 36M * 0 0 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1265 255 36M * 0 0 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1332 255 36M * 0 0 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4170 255 36M * 0 0 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2806 255 36M * 0 0 AATAATGTTTATGTTGGTTTCATGGTTTGGTCTAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3119 255 36M * 0 0 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1670 255 36M * 0 0 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 640 255 36M * 0 0 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2750 255 35M1H * 0 0 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4606 255 36M * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3573 255 36M * 0 0 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5105 255 36M * 0 0 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1674 255 36M * 0 0 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4095 255 36M * 0 0 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4551 255 36M * 0 0 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3284 255 36M * 0 0 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4005 255 36M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3045 255 1H35M * 0 0 GCTACCGATAACAATACTGTAGGCATGGGTGATGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1115 255 36M * 0 0 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1139 255 34M2H * 0 0 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 852 255 36M * 0 0 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5272 255 36M * 0 0 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4330 255 36M * 0 0 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4891 255 36M * 0 0 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4783 255 36M * 0 0 ATTTTATGCGGACACTTCCTACAGGTAGCGTTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3619 255 36M * 0 0 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4455 255 36M * 0 0 GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 632 255 36M * 0 0 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2964 255 35M1H * 0 0 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2763 255 36M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1719 255 36M * 0 0 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3100 255 36M * 0 0 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 598 255 35M1H * 0 0 GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4126 255 36M * 0 0 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4026 255 36M * 0 0 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2621 255 36M * 0 0 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2749 255 36M * 0 0 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 379 255 36M * 0 0 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2160 255 36M * 0 0 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1508 255 1H35M * 0 0 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3863 255 36M * 0 0 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5187 255 36M * 0 0 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4196 255 36M * 0 0 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 635 255 36M * 0 0 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1294 255 1H35M * 0 0 TAACACTACTGGTTATATTGACCATGCCGCTTTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5157 255 36M * 0 0 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 772 255 36M * 0 0 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1224 255 36M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1544 255 3H33M * 0 0 CGCCAAATGACGACTTCTACCACATCTATTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4840 255 36M * 0 0 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 204 255 35M1H * 0 0 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2481 255 36M * 0 0 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 332 255 36M * 0 0 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3978 255 36M * 0 0 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4865 255 36M * 0 0 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3271 255 36M * 0 0 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2738 255 36M * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2703 255 1H35M * 0 0 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2943 255 36M * 0 0 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3861 255 36M * 0 0 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3093 255 36M * 0 0 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3151 255 36M * 0 0 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 157 255 36M * 0 0 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4792 255 36M * 0 0 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3849 255 36M * 0 0 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2743 255 1H35M * 0 0 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3015 255 36M * 0 0 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1091 255 36M * 0 0 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 798 255 1H35M * 0 0 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4866 255 36M * 0 0 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4404 255 36M * 0 0 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1655 255 36M * 0 0 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5162 255 36M * 0 0 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1249 255 1H35M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3261 255 36M * 0 0 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3096 255 36M * 0 0 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2811 255 36M * 0 0 TGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3459 255 36M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 789 255 35M1H * 0 0 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3699 255 36M * 0 0 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2641 255 36M * 0 0 GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 305 255 36M * 0 0 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3066 255 35M1H * 0 0 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4428 255 36M * 0 0 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1461 255 36M * 0 0 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4000 255 36M * 0 0 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 220 255 36M * 0 0 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3194 255 36M * 0 0 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1266 255 35M1H * 0 0 GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4596 255 36M * 0 0 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1172 255 1H35M * 0 0 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1014 255 36M * 0 0 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2148 255 36M * 0 0 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5191 255 35M1H * 0 0 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 571 255 35M1H * 0 0 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 242 255 36M * 0 0 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 338 255 36M * 0 0 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1112 255 36M * 0 0 GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1254 255 2H34M * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2970 255 36M * 0 0 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5151 255 36M * 0 0 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 348 255 36M * 0 0 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4888 255 1H35M * 0 0 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3972 255 33M3H * 0 0 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5033 255 36M * 0 0 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1552 255 1H35M * 0 0 GACGACTTCTACCACATCTATTGACATTATGGGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1764 255 36M * 0 0 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1529 255 36M * 0 0 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4950 255 36M * 0 0 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4484 255 36M * 0 0 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4767 255 1H35M * 0 0 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 177 255 36M * 0 0 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2577 255 36M * 0 0 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 156 255 36M * 0 0 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 227 255 36M * 0 0 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 574 255 36M * 0 0 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3021 255 36M * 0 0 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3731 255 36M * 0 0 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2710 255 36M * 0 0 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4228 255 35M1H * 0 0 TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4606 255 34M2H * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 582 255 34M2H * 0 0 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1144 255 36M * 0 0 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1514 255 36M * 0 0 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1657 255 36M * 0 0 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1626 255 36M * 0 0 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3250 255 36M * 0 0 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1982 255 36M * 0 0 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2217 255 36M * 0 0 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3480 255 1H35M * 0 0 TCACGACAGAATACGAAAGACCAGGTATATGCACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1690 255 36M * 0 0 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4136 255 34M2H * 0 0 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4414 255 36M * 0 0 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3988 255 36M * 0 0 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4203 255 36M * 0 0 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4098 255 36M * 0 0 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4307 255 35M1H * 0 0 TATTAATAACACTATAGACCACCGCCCCGAAGGGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1521 255 35M1H * 0 0 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 945 255 36M * 0 0 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1575 255 36M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2099 255 36M * 0 0 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 524 255 36M * 0 0 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1252 255 36M * 0 0 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4916 255 36M * 0 0 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3828 255 36M * 0 0 GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3756 255 36M * 0 0 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1116 255 36M * 0 0 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3099 255 36M * 0 0 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3082 255 36M * 0 0 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 613 255 36M * 0 0 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 289 255 36M * 0 0 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4690 255 36M * 0 0 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3520 255 36M * 0 0 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3858 255 36M * 0 0 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3344 255 36M * 0 0 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4672 255 36M * 0 0 TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1800 255 36M * 0 0 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5077 255 36M * 0 0 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2763 255 1H35M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1203 255 36M * 0 0 TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5107 255 36M * 0 0 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5168 255 1H35M * 0 0 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2956 255 36M * 0 0 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 624 255 36M * 0 0 GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1877 255 1H35M * 0 0 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1214 255 36M * 0 0 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 558 255 36M * 0 0 GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3629 255 36M * 0 0 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2254 255 35M1H * 0 0 GACCACTCGCGATTCAATCATGACTTCGTGATAAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3001 255 36M * 0 0 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4667 255 35M1H * 0 0 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3464 255 36M * 0 0 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4911 255 35M1H * 0 0 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2222 255 36M * 0 0 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 646 255 35M1H * 0 0 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1364 255 36M * 0 0 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1613 255 1H35M * 0 0 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1045 255 35M1H * 0 0 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 339 255 36M * 0 0 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4937 255 36M * 0 0 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4344 255 2H34M * 0 0 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3674 255 36M * 0 0 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4945 255 36M * 0 0 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1946 255 36M * 0 0 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2662 255 36M * 0 0 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3313 255 36M * 0 0 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 727 255 36M * 0 0 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 555 255 36M * 0 0 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 485 255 36M * 0 0 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 318 255 36M * 0 0 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 910 255 36M * 0 0 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5005 255 36M * 0 0 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1379 255 36M * 0 0 GGTTATTTGAATATCTATAACAACTATTTTAAATCG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3168 255 36M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2738 255 33M3H * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4099 255 36M * 0 0 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2574 255 36M * 0 0 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2453 255 36M * 0 0 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5179 255 36M * 0 0 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3778 255 34M2H * 0 0 TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1843 255 36M * 0 0 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4637 255 36M * 0 0 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2225 255 36M * 0 0 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3368 255 36M * 0 0 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3311 255 36M * 0 0 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5039 255 36M * 0 0 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2059 255 36M * 0 0 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 388 255 36M * 0 0 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2754 255 36M * 0 0 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2128 255 36M * 0 0 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 154 255 36M * 0 0 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3617 255 36M * 0 0 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2775 255 36M * 0 0 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4217 255 36M * 0 0 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4619 255 35M1H * 0 0 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 411 255 35M1H * 0 0 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2730 255 35M1H * 0 0 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 521 255 35M1H * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4260 255 36M * 0 0 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1662 255 36M * 0 0 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 533 255 36M * 0 0 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 195 255 35M1H * 0 0 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2239 255 36M * 0 0 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1313 255 36M * 0 0 GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1545 255 36M * 0 0 GCCAAATGACGACTTCTACCACATCTATTGACATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 557 255 36M * 0 0 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1249 255 36M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 614 255 35M1H * 0 0 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 206 255 36M * 0 0 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4981 255 36M * 0 0 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1702 255 36M * 0 0 TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2321 255 35M1H * 0 0 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4088 255 35M1H * 0 0 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 900 255 36M * 0 0 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1155 255 36M * 0 0 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3587 255 36M * 0 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3787 255 36M * 0 0 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3834 255 35M1H * 0 0 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 989 255 36M * 0 0 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3712 255 36M * 0 0 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1207 255 36M * 0 0 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2116 255 36M * 0 0 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 660 255 36M * 0 0 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1536 255 36M * 0 0 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2112 255 1H35M * 0 0 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2816 255 36M * 0 0 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 5176 255 36M * 0 0 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3472 255 36M * 0 0 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1948 255 36M * 0 0 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2212 255 35M1H * 0 0 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3817 255 35M1H * 0 0 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3563 255 36M * 0 0 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4198 255 1H35M * 0 0 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2907 255 1H35M * 0 0 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2843 255 35M1H * 0 0 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4374 255 36M * 0 0 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1940 255 1H35M * 0 0 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5073 255 36M * 0 0 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4434 255 36M * 0 0 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1274 255 1H35M * 0 0 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4440 255 36M * 0 0 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3920 255 36M * 0 0 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4587 255 1H35M * 0 0 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1707 255 36M * 0 0 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1582 255 36M * 0 0 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2698 255 36M * 0 0 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3167 255 36M * 0 0 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2289 255 36M * 0 0 AGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1012 255 36M * 0 0 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 161 255 36M * 0 0 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1165 255 1H35M * 0 0 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5010 255 36M * 0 0 GTGGATAAATACGTTAACAAAAAGTCAGATATGGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2286 255 36M * 0 0 AAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 801 255 36M * 0 0 GCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1587 255 36M * 0 0 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4578 255 36M * 0 0 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3570 255 36M * 0 0 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 496 255 36M * 0 0 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4754 255 36M * 0 0 TAATGGCCGTCTTCATTTCCATGCGGTGCATTTTAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4235 255 35M1H * 0 0 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2293 255 36M * 0 0 TGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1579 255 1H35M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3332 255 36M * 0 0 TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4132 255 36M * 0 0 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4775 255 36M * 0 0 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1 255 4H32M * 0 0 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 54 255 36M * 0 0 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 231 255 36M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4192 255 36M * 0 0 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1580 255 36M * 0 0 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 611 255 36M * 0 0 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4532 255 1H35M * 0 0 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 638 255 35M1H * 0 0 TTATTATGTTCATCCCGTCAACATTCAAACTGCCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1957 255 36M * 0 0 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3979 255 36M * 0 0 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 540 255 1H35M * 0 0 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1852 255 36M * 0 0 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4684 255 36M * 0 0 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3690 255 36M * 0 0 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 584 255 36M * 0 0 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3852 255 1H35M * 0 0 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2857 255 35M1H * 0 0 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4658 255 35M1H * 0 0 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1721 255 36M * 0 0 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1954 255 36M * 0 0 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 962 255 36M * 0 0 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2175 255 36M * 0 0 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2442 255 36M * 0 0 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5126 255 1H35M * 0 0 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 5206 255 36M * 0 0 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2879 255 36M * 0 0 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2004 255 36M * 0 0 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2154 255 36M * 0 0 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1093 255 35M1H * 0 0 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3127 255 36M * 0 0 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3544 255 36M * 0 0 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2508 255 35M1H * 0 0 ATCGTCAACGTTATATTTTGATAGTTTGACGTTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3600 255 36M * 0 0 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1734 255 36M * 0 0 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2655 255 33M3H * 0 0 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2934 255 36M * 0 0 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1522 255 36M * 0 0 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4063 255 36M * 0 0 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3395 255 36M * 0 0 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 409 255 36M * 0 0 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1867 255 36M * 0 0 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3780 255 36M * 0 0 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3982 255 36M * 0 0 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2815 255 36M * 0 0 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1242 255 36M * 0 0 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4659 255 1H35M * 0 0 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 527 255 35M1H * 0 0 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4817 255 36M * 0 0 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2100 255 36M * 0 0 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2762 255 36M * 0 0 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4955 255 36M * 0 0 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3761 255 36M * 0 0 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4499 255 36M * 0 0 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4039 255 36M * 0 0 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4788 255 36M * 0 0 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4381 255 36M * 0 0 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4256 255 36M * 0 0 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 10 255 1H35M * 0 0 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1579 255 36M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3862 255 36M * 0 0 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3278 255 36M * 0 0 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 349 255 36M * 0 0 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG * -HWI-EAS91_1_306UPAAXX 0 PHIX174 4608 255 36M * 0 0 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 3808 255 35M1H * 0 0 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4753 255 36M * 0 0 CTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 286 255 36M * 0 0 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2850 255 36M * 0 0 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4740 255 36M * 0 0 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2467 255 1H35M * 0 0 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 320 255 34M2H * 0 0 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 521 255 36M * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 333 255 36M * 0 0 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA * -HWI-EAS91_1_306UPAAXX 0 PHIX174 2756 255 36M * 0 0 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4957 255 36M * 0 0 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 72 255 36M * 0 0 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4249 255 36M * 0 0 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 2592 255 36M * 0 0 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 1974 255 36M * 0 0 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT * -HWI-EAS91_1_306UPAAXX 16 PHIX174 3540 255 36M * 0 0 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA * -HWI-EAS91_1_306UPAAXX 16 PHIX174 4130 255 36M * 0 0 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4295 255 1H35M * 0 0 CCCCCAACTTGATATTAATAACACTATAGACCACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3522 255 36M * 0 0 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 229 255 36M * 0 0 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1067 255 1H35M * 0 0 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1788 255 36M * 0 0 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4563 255 36M * 0 0 GGTTGGTTTATCGTTTTTGACACTCTCACGTTGTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2668 255 36M * 0 0 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4248 255 36M * 0 0 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2511 255 34M2H * 0 0 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5152 255 36M * 0 0 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4884 255 36M * 0 0 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 5052 255 36M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4909 255 36M * 0 0 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2863 255 36M * 0 0 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4173 255 36M * 0 0 GTTGAGTTCGATAATGGTGATATGTATGTTTACGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1701 255 36M * 0 0 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1683 255 36M * 0 0 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3126 255 1H35M * 0 0 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1665 255 36M * 0 0 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3213 255 36M * 0 0 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3420 255 36M * 0 0 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 513 255 36M * 0 0 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2879 255 36M * 0 0 ATAAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4471 255 36M * 0 0 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1229 255 36M * 0 0 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 615 255 36M * 0 0 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 257 255 36M * 0 0 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2381 255 36M * 0 0 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4098 255 36M * 0 0 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5099 255 36M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3408 255 36M * 0 0 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 4043 255 36M * 0 0 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4560 255 36M * 0 0 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1888 255 36M * 0 0 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3434 255 1H35M * 0 0 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4539 255 36M * 0 0 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1828 255 36M * 0 0 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3708 255 36M * 0 0 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3326 255 36M * 0 0 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4176 255 36M * 0 0 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 22 255 36M * 0 0 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2557 255 36M * 0 0 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3277 255 36M * 0 0 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3592 255 36M * 0 0 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 358 255 35M1H * 0 0 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1775 255 36M * 0 0 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3504 255 36M * 0 0 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1554 255 36M * 0 0 CGACTTCTACCACATCTATTGACATTATGGGTCTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3626 255 36M * 0 0 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3572 255 36M * 0 0 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1265 255 36M * 0 0 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1332 255 36M * 0 0 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4254 255 36M * 0 0 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4170 255 36M * 0 0 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2806 255 36M * 0 0 AATAATGTTTATGTTGGTTTCATGGTTTGGTCTAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3119 255 36M * 0 0 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1670 255 36M * 0 0 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 640 255 36M * 0 0 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2750 255 35M1H * 0 0 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4606 255 36M * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3573 255 36M * 0 0 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5105 255 36M * 0 0 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1674 255 36M * 0 0 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4095 255 36M * 0 0 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4551 255 36M * 0 0 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3284 255 36M * 0 0 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4005 255 36M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3045 255 1H35M * 0 0 GCTACCGATAACAATACTGTAGGCATGGGTGATGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1115 255 36M * 0 0 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1139 255 34M2H * 0 0 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 852 255 36M * 0 0 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5272 255 36M * 0 0 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4330 255 36M * 0 0 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4891 255 36M * 0 0 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4783 255 36M * 0 0 ATTTTATGCGGACACTTCCTACAGGTAGCGTTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3619 255 36M * 0 0 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4455 255 36M * 0 0 GGTATTAAGGATGAGTGTTCAAGATTGCTGGATGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 632 255 36M * 0 0 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2964 255 35M1H * 0 0 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2763 255 36M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1719 255 36M * 0 0 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3100 255 36M * 0 0 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 598 255 35M1H * 0 0 GCTTTCCTGCTCCTGTTGAGTTTATTGCTTCCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4126 255 36M * 0 0 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4026 255 36M * 0 0 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2621 255 36M * 0 0 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2749 255 36M * 0 0 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 379 255 36M * 0 0 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2160 255 36M * 0 0 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1508 255 1H35M * 0 0 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3863 255 36M * 0 0 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5187 255 36M * 0 0 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4196 255 36M * 0 0 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 635 255 36M * 0 0 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1294 255 1H35M * 0 0 TAACACTACTGGTTATATTGACCATGCCGCTTTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5157 255 36M * 0 0 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 772 255 36M * 0 0 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1224 255 36M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1544 255 3H33M * 0 0 CGCCAAATGACGACTTCTACCACATCTATTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4840 255 36M * 0 0 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 204 255 35M1H * 0 0 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2481 255 36M * 0 0 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 332 255 36M * 0 0 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3978 255 36M * 0 0 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4865 255 36M * 0 0 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3271 255 36M * 0 0 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2738 255 36M * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2703 255 1H35M * 0 0 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2943 255 36M * 0 0 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3861 255 36M * 0 0 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3093 255 36M * 0 0 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3151 255 36M * 0 0 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1193 255 36M * 0 0 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 157 255 36M * 0 0 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4792 255 36M * 0 0 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3849 255 36M * 0 0 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2743 255 1H35M * 0 0 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3015 255 36M * 0 0 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1091 255 36M * 0 0 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 798 255 1H35M * 0 0 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4866 255 36M * 0 0 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4404 255 36M * 0 0 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1655 255 36M * 0 0 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5162 255 36M * 0 0 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1249 255 1H35M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3261 255 36M * 0 0 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3096 255 36M * 0 0 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2811 255 36M * 0 0 TGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3459 255 36M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG * +HWI-EAS91_1_306UPAAXX 0 phiX174 789 255 35M1H * 0 0 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3699 255 36M * 0 0 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2641 255 36M * 0 0 GCCGACCCTAAATTTTTTGCCTGTTTGGTTCTCTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 305 255 36M * 0 0 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3066 255 35M1H * 0 0 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4428 255 36M * 0 0 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1461 255 36M * 0 0 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4000 255 36M * 0 0 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 220 255 36M * 0 0 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3194 255 36M * 0 0 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1266 255 35M1H * 0 0 GTGTTAATGCCACTCCTCTCCCGACTGTTAACTCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4596 255 36M * 0 0 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1172 255 1H35M * 0 0 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 636 255 36M * 0 0 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2873 255 36M * 0 0 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1014 255 36M * 0 0 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2148 255 36M * 0 0 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5191 255 35M1H * 0 0 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1590 255 36M * 0 0 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 571 255 35M1H * 0 0 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 242 255 36M * 0 0 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 338 255 36M * 0 0 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1112 255 36M * 0 0 GCTGGCGACTCCTTCGAGATGGACGCCGTTTGCGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1254 255 2H34M * 0 0 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2970 255 36M * 0 0 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5151 255 36M * 0 0 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 348 255 36M * 0 0 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4888 255 1H35M * 0 0 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3972 255 33M3H * 0 0 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5033 255 36M * 0 0 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1552 255 1H35M * 0 0 GACGACTTCTACCACATCTATTGACATTATGGGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1764 255 36M * 0 0 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1529 255 36M * 0 0 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4950 255 36M * 0 0 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4484 255 36M * 0 0 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4767 255 1H35M * 0 0 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 177 255 36M * 0 0 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2577 255 36M * 0 0 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 156 255 36M * 0 0 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 227 255 36M * 0 0 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 574 255 36M * 0 0 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3021 255 36M * 0 0 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3731 255 36M * 0 0 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2710 255 36M * 0 0 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4228 255 35M1H * 0 0 TTCGTGATGAGTTTGTATCTGTTACTGATAAGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4606 255 34M2H * 0 0 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2766 255 36M * 0 0 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 582 255 34M2H * 0 0 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1144 255 36M * 0 0 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1514 255 36M * 0 0 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1657 255 36M * 0 0 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2071 255 36M * 0 0 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1626 255 36M * 0 0 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3250 255 36M * 0 0 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1982 255 36M * 0 0 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2217 255 36M * 0 0 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3480 255 1H35M * 0 0 TCACGACAGAATACGAAAGACCAGGTATATGCACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1690 255 36M * 0 0 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4136 255 34M2H * 0 0 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4414 255 36M * 0 0 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3988 255 36M * 0 0 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4203 255 36M * 0 0 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 4098 255 36M * 0 0 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4307 255 35M1H * 0 0 TATTAATAACACTATAGACCACCGCCCCGAAGGGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1521 255 35M1H * 0 0 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 945 255 36M * 0 0 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1575 255 36M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2689 255 36M * 0 0 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2099 255 36M * 0 0 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 524 255 36M * 0 0 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1252 255 36M * 0 0 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4916 255 36M * 0 0 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3828 255 36M * 0 0 GGTATTGATAAAGCTGTTGCCGATACTTGTAACAAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3756 255 36M * 0 0 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1116 255 36M * 0 0 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3099 255 36M * 0 0 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3082 255 36M * 0 0 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 613 255 36M * 0 0 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 289 255 36M * 0 0 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4690 255 36M * 0 0 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3520 255 36M * 0 0 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3858 255 36M * 0 0 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3344 255 36M * 0 0 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4672 255 36M * 0 0 TTCTTGCTGCCGAGGGTCGCAAGGCTATTGTTTCAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1800 255 36M * 0 0 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 5077 255 36M * 0 0 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2763 255 1H35M * 0 0 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4282 255 36M * 0 0 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1203 255 36M * 0 0 TTACTTTTTATGTCCCTCATCGTCACGTTTATGTTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 5107 255 36M * 0 0 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5168 255 1H35M * 0 0 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2956 255 36M * 0 0 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 624 255 36M * 0 0 GCTGCCGTCATTGCTTATTATGTTCATCCCTTCAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1877 255 1H35M * 0 0 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1214 255 36M * 0 0 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT * +HWI-EAS91_1_306UPAAXX 0 phiX174 558 255 36M * 0 0 GCTTGCGTTTATGGTACGCTGGACTTTTTGTGATAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3629 255 36M * 0 0 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2254 255 35M1H * 0 0 GACCACTCGCGATTCAATCATGACTTCGTGATAAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2479 255 36M * 0 0 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3001 255 36M * 0 0 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4667 255 35M1H * 0 0 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3464 255 36M * 0 0 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4911 255 35M1H * 0 0 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2222 255 36M * 0 0 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 646 255 35M1H * 0 0 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1364 255 36M * 0 0 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1613 255 1H35M * 0 0 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1045 255 35M1H * 0 0 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 339 255 36M * 0 0 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4937 255 36M * 0 0 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4344 255 2H34M * 0 0 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3674 255 36M * 0 0 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4945 255 36M * 0 0 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 1946 255 36M * 0 0 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2662 255 36M * 0 0 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCTACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3313 255 36M * 0 0 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 727 255 36M * 0 0 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 555 255 36M * 0 0 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 485 255 36M * 0 0 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 318 255 36M * 0 0 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 910 255 36M * 0 0 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4936 255 36M * 0 0 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5005 255 36M * 0 0 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1379 255 36M * 0 0 GGTTATTTGAATATCTATAACAACTATTTTAAATCG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3168 255 36M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGTCTGGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2738 255 33M3H * 0 0 GCCATGATGGTGGTTATTATACCGTCAAGGACT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4099 255 36M * 0 0 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2574 255 36M * 0 0 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2453 255 36M * 0 0 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 5179 255 36M * 0 0 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 3778 255 34M2H * 0 0 TTTCTAATGTCGTCACTGATGCTGCTTCTGTTGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1843 255 36M * 0 0 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1082 255 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4637 255 36M * 0 0 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2225 255 36M * 0 0 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3368 255 36M * 0 0 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3311 255 36M * 0 0 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5039 255 36M * 0 0 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2059 255 36M * 0 0 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 388 255 36M * 0 0 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2754 255 36M * 0 0 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2128 255 36M * 0 0 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 154 255 36M * 0 0 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3617 255 36M * 0 0 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2775 255 36M * 0 0 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4217 255 36M * 0 0 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4619 255 35M1H * 0 0 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 411 255 35M1H * 0 0 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2730 255 35M1H * 0 0 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 521 255 35M1H * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4260 255 36M * 0 0 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1662 255 36M * 0 0 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 533 255 36M * 0 0 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 195 255 35M1H * 0 0 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2239 255 36M * 0 0 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1313 255 36M * 0 0 GACCATGCCGCTTTTCTTGGCACGATTAACCCTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1545 255 36M * 0 0 GCCAAATGACGACTTCTACCACATCTATTGACATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 557 255 36M * 0 0 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1249 255 36M * 0 0 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4174 255 36M * 0 0 TTGAGTTCGATAATGGTGATATGTATGTTGACGTCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 614 255 35M1H * 0 0 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 206 255 36M * 0 0 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4981 255 36M * 0 0 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1702 255 36M * 0 0 TCCTTTACTTGTCATGCGCTCTAATCTCTGTGCATC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2321 255 35M1H * 0 0 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4088 255 35M1H * 0 0 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG * +HWI-EAS91_1_306UPAAXX 0 phiX174 900 255 36M * 0 0 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1155 255 36M * 0 0 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3587 255 36M * 0 0 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3787 255 36M * 0 0 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3834 255 35M1H * 0 0 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 989 255 36M * 0 0 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3712 255 36M * 0 0 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1207 255 36M * 0 0 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2116 255 36M * 0 0 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 660 255 36M * 0 0 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1536 255 36M * 0 0 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2112 255 1H35M * 0 0 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2816 255 36M * 0 0 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 5176 255 36M * 0 0 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 3472 255 36M * 0 0 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1948 255 36M * 0 0 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2212 255 35M1H * 0 0 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3817 255 35M1H * 0 0 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3563 255 36M * 0 0 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4198 255 1H35M * 0 0 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2907 255 1H35M * 0 0 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2843 255 35M1H * 0 0 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4374 255 36M * 0 0 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTGTACGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1940 255 1H35M * 0 0 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5073 255 36M * 0 0 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4434 255 36M * 0 0 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1274 255 1H35M * 0 0 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4440 255 36M * 0 0 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3920 255 36M * 0 0 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4587 255 1H35M * 0 0 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1707 255 36M * 0 0 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1582 255 36M * 0 0 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1588 255 36M * 0 0 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2698 255 36M * 0 0 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3167 255 36M * 0 0 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2289 255 36M * 0 0 AGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1012 255 36M * 0 0 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 161 255 36M * 0 0 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1165 255 1H35M * 0 0 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA * +HWI-EAS91_1_306UPAAXX 16 phiX174 5010 255 36M * 0 0 GTGGATAAATACGTTAACAAAAAGTCAGATATGGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2286 255 36M * 0 0 AAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 801 255 36M * 0 0 GCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1587 255 36M * 0 0 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4578 255 36M * 0 0 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3570 255 36M * 0 0 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 496 255 36M * 0 0 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 441 255 36M * 0 0 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4754 255 36M * 0 0 TAATGGCCGTCTTCATTTCCATGCGGTGCATTTTAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4235 255 35M1H * 0 0 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2293 255 36M * 0 0 TGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1579 255 1H35M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3332 255 36M * 0 0 TGGTGCTGATGCTTCCTCTGCTGGTATGGTTTACGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4132 255 36M * 0 0 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4775 255 36M * 0 0 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1 255 4H32M * 0 0 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 54 255 36M * 0 0 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 231 255 36M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 4192 255 36M * 0 0 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 1580 255 36M * 0 0 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT * +HWI-EAS91_1_306UPAAXX 16 phiX174 611 255 36M * 0 0 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4532 255 1H35M * 0 0 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 638 255 35M1H * 0 0 TTATTATGTTCATCCCGTCAACATTCAAACTGCCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1957 255 36M * 0 0 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2728 255 36M * 0 0 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3979 255 36M * 0 0 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG * +HWI-EAS91_1_306UPAAXX 16 phiX174 540 255 1H35M * 0 0 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 1852 255 36M * 0 0 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4684 255 36M * 0 0 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3690 255 36M * 0 0 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCATCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 584 255 36M * 0 0 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3852 255 1H35M * 0 0 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2857 255 35M1H * 0 0 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1728 255 36M * 0 0 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC * +HWI-EAS91_1_306UPAAXX 0 phiX174 4658 255 35M1H * 0 0 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1721 255 36M * 0 0 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1954 255 36M * 0 0 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC * +HWI-EAS91_1_306UPAAXX 0 phiX174 962 255 36M * 0 0 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 2175 255 36M * 0 0 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2442 255 36M * 0 0 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 5126 255 1H35M * 0 0 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 5206 255 36M * 0 0 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2879 255 36M * 0 0 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 2004 255 36M * 0 0 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG * +HWI-EAS91_1_306UPAAXX 0 phiX174 2154 255 36M * 0 0 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1093 255 35M1H * 0 0 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG * +HWI-EAS91_1_306UPAAXX 16 phiX174 3127 255 36M * 0 0 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3544 255 36M * 0 0 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2508 255 35M1H * 0 0 ATCGTCAACGTTATATTTTGATAGTTTGACGTTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3600 255 36M * 0 0 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1734 255 36M * 0 0 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2655 255 33M3H * 0 0 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 2934 255 36M * 0 0 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1522 255 36M * 0 0 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4063 255 36M * 0 0 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3395 255 36M * 0 0 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 409 255 36M * 0 0 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1867 255 36M * 0 0 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 3780 255 36M * 0 0 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTGTTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3982 255 36M * 0 0 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2815 255 36M * 0 0 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 1242 255 36M * 0 0 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4659 255 1H35M * 0 0 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2436 255 36M * 0 0 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC * +HWI-EAS91_1_306UPAAXX 0 phiX174 527 255 35M1H * 0 0 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4817 255 36M * 0 0 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2100 255 36M * 0 0 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG * +HWI-EAS91_1_306UPAAXX 16 phiX174 2762 255 36M * 0 0 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA * +HWI-EAS91_1_306UPAAXX 0 phiX174 4955 255 36M * 0 0 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 3761 255 36M * 0 0 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4499 255 36M * 0 0 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4039 255 36M * 0 0 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4788 255 36M * 0 0 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT * +HWI-EAS91_1_306UPAAXX 0 phiX174 1002 255 36M * 0 0 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4381 255 36M * 0 0 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4256 255 36M * 0 0 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 10 255 1H35M * 0 0 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1579 255 36M * 0 0 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC * +HWI-EAS91_1_306UPAAXX 0 phiX174 3862 255 36M * 0 0 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3278 255 36M * 0 0 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT * +HWI-EAS91_1_306UPAAXX 0 phiX174 349 255 36M * 0 0 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG * +HWI-EAS91_1_306UPAAXX 0 phiX174 4608 255 36M * 0 0 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT * +HWI-EAS91_1_306UPAAXX 0 phiX174 3808 255 35M1H * 0 0 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 4753 255 36M * 0 0 CTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 286 255 36M * 0 0 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT * +HWI-EAS91_1_306UPAAXX 0 phiX174 2850 255 36M * 0 0 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT * +HWI-EAS91_1_306UPAAXX 16 phiX174 680 255 1H35M * 0 0 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4740 255 36M * 0 0 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2467 255 1H35M * 0 0 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA * +HWI-EAS91_1_306UPAAXX 0 phiX174 320 255 34M2H * 0 0 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA * +HWI-EAS91_1_306UPAAXX 0 phiX174 1180 255 34M2H * 0 0 TATTGACTCTACTGTAGACATTTTTACTTTTTAT * +HWI-EAS91_1_306UPAAXX 16 phiX174 521 255 36M * 0 0 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 333 255 36M * 0 0 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA * +HWI-EAS91_1_306UPAAXX 0 phiX174 2756 255 36M * 0 0 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC * +HWI-EAS91_1_306UPAAXX 16 phiX174 4957 255 36M * 0 0 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA * +HWI-EAS91_1_306UPAAXX 16 phiX174 72 255 36M * 0 0 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4249 255 36M * 0 0 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT * +HWI-EAS91_1_306UPAAXX 16 phiX174 2592 255 36M * 0 0 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA * +HWI-EAS91_1_306UPAAXX 16 phiX174 1974 255 36M * 0 0 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT * +HWI-EAS91_1_306UPAAXX 16 phiX174 3540 255 36M * 0 0 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA * +HWI-EAS91_1_306UPAAXX 16 phiX174 4130 255 36M * 0 0 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT * --- a/test-data/perm_out4.sam +++ b/test-data/perm_out4.sam @@ -1,53 +1,55 @@ -1831_573_1219 16 phiX 2201 255 35M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC -A@EE>NVA7FQZSC8GRJK<EVGC<==39BP\__ NM:i:0 CS:Z:G1211130300300301021212330201121310 CQ:Z:@@@=4/+)5)408?'665>*/5?<61';<3,:,5- -1831_573_1242 0 phiX 647 255 35M * 0 0 TCATCCCGTCAACATTCAAACGGCCTGTCTCATCA [[WSWNGS]US^_\WQW]WL?CEMUIMSTSJ*1U; NM:i:1 CS:Z:T2132003121011302100130302112221121 CQ:Z:>>>::>17=A5?@@=;7A=;2.60>82<8=74+;; -1831_573_1647 16 phiX 1117 255 35M * 0 0 CGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC 4NIKVOPIBACPWOQ^^WSZ_\Y][Y]]^_[[_^[ NM:i:0 CS:Z:G0222233301013033120132223202022123 CQ:Z:=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -1831_573_1684 16 phiX 3695 255 35M * 0 0 TAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGC ?\VWTLTTUZVV[_^\Y[_ZWUW]^_XKR[SQJNT NM:i:0 CS:Z:G3310013212312012302121010221231123 CQ:Z:7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -1831_574_109 0 phiX 3728 255 35M * 0 0 GCAGAATCAGCGGTATGGCTCTTCTCATATTGGCG 07651#4817>@65<2:84716=788<1995.7?6 NM:i:1 CS:Z:G3122332123301331032220222133301033 CQ:Z:07651#4817>@65<2:84716=788<1995.7?6 -1831_574_148 16 phiX 2368 255 35M * 0 0 GTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCA ;NEGQTTTJAMH9B@@PHHSQUJML=LPMUMPJGV NM:i:0 CS:Z:T1200113123030012202302312200010231 CQ:Z:<;->3;;3>//>0;;7=,=4-4/+>029<9<624; -1831_574_575 16 phiX 4005 255 35M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTAT <JC>=PXK;2BW[T;CXA"&?U\\__WU]^[Z]^U NM:i:1 CS:Z:A3313322100212102033032123311211302 CQ:Z:7?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -1831_574_592 16 phiX 2949 255 35M * 0 0 GGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCAT 2BBLI?LTSPIFFIMD:?MRLECQ][G7DI9=A?I NM:i:0 CS:Z:A3103330110123102223122023103310330 CQ:Z:73-5)19,,<@>4067<2.-864346;9<1/;212 -1831_574_824 16 phiX 3996 255 35M * 0 0 TACCCTTCTGAATGTCACGCTGATTATTTTGACTT ?VRCD\ZK5?ZWJ7D]WP=AVQRHH[J64CUZ__Z NM:i:0 CS:Z:A0212100033032123311211302122020013 CQ:Z:;@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -1831_574_1194 0 phiX 1135 255 35M * 0 0 CGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTC NRXFJ]WXXX^^PP_\\RO\]]SR^_XLRUKC:A6 NM:i:0 CS:Z:C3303101033322220312200222013013312 CQ:Z::5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -1831_574_1591 16 phiX 5117 255 35M * 0 0 GAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCG 9CB??UTRA!7YIJXQUSUEEZWX[WNV^ZY^\XY NM:i:1 CS:Z:C3202101330322130221230222201123202 CQ:Z:==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -1831_574_1624 16 phiX 4057 255 35M * 0 0 CTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAA )5?C6:LSC5DHJA6@FNI54;D?137CB3-3CQ: NM:i:1 CS:Z:C0122200222132200313011102302210332 CQ:Z:#<6.&(,7-+))7..'/;43.)927.(<85&13-) -1831_574_1903 0 phiX 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC TMJT^]XQV__WQY]UUYXUVVV]QNSGOOJOPI/ NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -1831_575_54 16 phiX 3586 255 35M * 0 0 TTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGC 8ST4/MPK:7HONA7BTVCHY[^YRSVLMSMU_\Z NM:i:1 CS:Z:G3331330322230200102132110132013200 CQ:Z:>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -1831_575_197 16 phiX 4860 255 35M * 0 0 AGCTTGCAAAATACGTGGCCTTATGGTTACAGTAT ,=.<SADLUZH>67?JXRIFRTTVOQZ`RHIRXF8 NM:i:1 CS:Z:A3312113010133020301131330001310032 CQ:Z:,-:?463@A:88?6?437<=.2&1.;@67.4@%2, -1831_575_444 16 phiX 5097 255 35M * 0 0 AAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAAT >XO0/QUSCCY]]LJWZ^[W\ZVGF[^[JIVZ_QM NM:i:1 CS:Z:A3022120112320220100202132332113320 CQ:Z:<2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -1831_575_622 0 phiX 2484 255 35M * 0 0 TGTTTTACAGACACCTAAAGCTACATCGTCAACGT `XY^\_^Z[^ZY[Z[WNQOLO?DOBJB@M>EQ$!+ NM:i:1 CS:Z:T1100031122111023002323113231210111 CQ:Z:@A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -1831_575_938 16 phiX 1132 255 35M * 0 0 GGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGC 7N@<NSTMKOQVHAONKTXVTUWZXRTWZ^XY_YT NM:i:0 CS:Z:G3103102220022130222233301013033120 CQ:Z:;:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -1831_575_970 16 phiX 231 255 35M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCG 5PXYYNKY^\[VW[\]XY[VUTRY_[Y]_ZW\\\\ NM:i:0 CS:Z:C3201311301023133303023011202220221 CQ:Z:=@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -1831_575_1138 0 phiX 1912 255 35M * 0 0 CGCTAAAGGTGCTTTGACTTATACCGATATTGCTG XLJ7-IKH@IWNTJJSPUKO]UU[UTNQKDQDCJ1 NM:i:1 CS:Z:C3320002011320012120333103233301321 CQ:Z:<=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -1831_575_1180 0 phiX 4168 255 35M * 0 0 AGGGCGTTGAGTTCGATAATGGTGATATGTATGTT J]_RSE@HENVYKKOINRQOV_]VLPSRLHMBJT7 NM:i:0 CS:Z:A2003310122102323303101123331133110 CQ:Z:/<B>5?':/78?;1;55:997@@>94=7<186->7 -1831_575_1302 16 phiX 5201 255 35M * 0 0 ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCA *57==/2(a)B6+-8?,!,.(.A=+*7>2,841LOB6 NM:i:1 CS:Z:T1201303312333123130200123201013021 CQ:Z:&12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -1831_575_1310 16 phiX 1611 255 35M * 0 0 ATACTGACCAAGAACGTGATTACTTCATGCAGCGT ;QC!!DXV[[Z]UEN_YYPAMSVGGXQWQHKSYWQ NM:i:1 CS:Z:A1332131312021303211310220101211133 CQ:Z:6<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -1831_575_1321 0 phiX 2663 255 35M * 0 0 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACT 0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 NM:i:1 CS:Z:G1001010233200122122022023000203212 CQ:Z:0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -1831_575_1373 16 phiX 4220 255 35M * 0 0 TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTG <M=?PSE>BHTUGKZZZYY]]VU]^[TUWZ]]__` NM:i:0 CS:Z:C1213011223311001221321132013121220 CQ:Z:A@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -1831_575_1436 0 phiX 3459 255 35M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATAC ;Q\WMKB<NE=OUWRFO[V?=PUXC6LZN77CHQ< NM:i:0 CS:Z:G3210313021212303321202113301220331 CQ:Z:*2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -1831_575_1442 0 phiX 3316 255 35M * 0 0 ATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT URLSZUTH;RWB;GTWUNS\^ZJP^SGKFMSB?N> NM:i:0 CS:Z:A3132010022331132101132123132020222 CQ:Z:8>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -1831_575_1500 16 phiX 4268 255 35M * 0 0 TGAATTGGCACAATGCTACAATGTGCTCCCCCAAC 9V\UBGWPPNT^YUQQQQUQLPRUQQSV^`_^_^P NM:i:0 CS:Z:G1010000223111301132313011130103021 CQ:Z:2?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -1831_575_1535 16 phiX 1224 255 35M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATG <PRXVWQOTQUST^[\WMT^]Z\_`ZX`a_[[\^a NM:i:0 CS:Z:C1312012030320112110211013300131121 CQ:Z:@B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -1831_576_86 16 phiX 2980 255 35M * 0 0 CCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCC /@:AJ7;AEH712=EJKF>=LHJP?587CK:9AHN NM:i:0 CS:Z:G0320000121033022010011030032211310 CQ:Z:7811)2:*.++5</:3+43924*))/:,6&29)2/ -1831_576_266 16 phiX 279 255 35M * 0 0 TAGATATGAGTCACATTTTGTTCATGGTAGAGATT 6;*<NGC9=TWH2<P=+#.P]IDV]\SUZVW[^_[ NM:i:1 CS:Z:A0322223101312011300311121221333223 CQ:Z:<@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -1831_576_603 16 phiX 1575 255 35M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTG 8PMKX]PIR\`ZJO]_[HGZ_XOW\Z]LPb\RIS_ NM:i:0 CS:Z:C1003032313302312320131221001330311 CQ:Z:@@46=@C.??<A79@@;-<@@>29B?>55<B7598 -1831_576_655 16 phiX 3291 255 35M * 0 0 CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGA %06ESGLVW^JATXW73V][JCT_]G?Q[_XYa`\ NM:i:1 CS:Z:T2001023130302322122200313123123102 CQ:Z:=@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -1831_576_815 0 phiX 5185 255 35M * 0 0 CGGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC NP]^WV]^`^ZZWX^_]][ZWKFQPA?FSTQPKD. NM:i:0 CS:Z:C3022113203032010120310102321001031 CQ:Z:<3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -1831_576_882 0 phiX 5052 255 35M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTC PGTVV^YMQ]]VNT]ZWXQ;7LYVPKIRXTTLNU8 NM:i:0 CS:Z:G3230020122320223230022031020110122 CQ:Z:?26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -1831_576_898 0 phiX 517 255 35M * 0 0 GGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGC \_bTPa`\ZY]WOMW`YYLL]VNS^]SSLES][J. NM:i:0 CS:Z:G0230132312121033222231132231233213 CQ:Z:=@@C2?C>?<>@886B?;?.??87=B<8<15??=. -1831_576_923 0 phiX 1049 255 35M * 0 0 CATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCT LCBEMWHCNQTTNSXUNLTVUKAKV[TMRRURIJ7 NM:i:0 CS:Z:C1322010320202013210121223010123122 CQ:Z:76.51=;.699<96>;;49<;;11;<@59:9=647 -1831_576_1131 16 phiX 4060 255 35M * 0 0 TTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCC <MJBDSMK>BWZI2FPGKEOI<PWVQ?KNN>>SC@ NM:i:1 CS:Z:G0233122200222132200313011102302210 CQ:Z:104@#@/@,4>9?2+?1571@',>=;(759;*92< -1831_576_1289 16 phiX 1898 255 35M * 0 0 ATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTA 0DBK[ONJ9GWSQ@;@CINYOHKU_VQZ_aRNYTX NM:i:0 CS:Z:T3021210023110200323310302013121203 CQ:Z:@9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -1831_576_1367 0 phiX 1838 255 35M * 0 0 GAGCATGGCACTATGTTTACTCTTGCGCTTGTTCG ]^_[Y]_\\[[[X\]]^]WRXZXZZXSROMXVNN7 NM:i:0 CS:Z:G2231310311233110031222013332011023 CQ:Z:??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -1831_576_1416 0 phiX 4521 255 35M * 0 0 ATTCAGCGTTTGATGAATGCAATGCGACAGGCTCA 1AYL;>>I[F4JG@CBSURK<KUQB,AZRJCFPW@ NM:i:0 CS:Z:A3021233100123120313103133211203221 CQ:Z:+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -1831_576_1605 0 phiX 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC Q[bb_]NKZYTVW[_XX^]]WTNQSA>BMPKNMB, NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:6<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -1831_576_1729 16 phiX 5193 255 35M * 0 0 TTAATCCAACTTACCAAGCTGGGTTACGACGCGAC >ZL:FYXSQV]^ZSW^\TU\\[YKM_^][ZZZ^^^ NM:i:0 CS:Z:G1233312313010012320101302101023030 CQ:Z:@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -1831_576_1982 16 phiX 5023 255 35M * 0 0 TTAACAAAAAGTCAGATATGGACCTTGCTGCTAAA @JFRDK\_\MQUU_UQST^ZX^[\XX[Y^LK^^_K NM:i:0 CS:Z:T0032312310201201333221212000011030 CQ:Z:,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -1831_577_133 16 phiX 1713 255 35M * 0 0 TCATGCGCTCTAATCTCTGGGCATCTGGCTATGAT )&/8<NA=EPP;FEI]YY]_VFO]HDXOM[\[]SB NM:i:1 CS:Z:A3213323012231300122223032223331322 CQ:Z:/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -1831_577_281 16 phiX 4576 255 35M * 0 0 TTTTTGACACTCTCACGTTGGCTGACGACCGATTA ?XWE?WXSYURPOYWMJ@I[[RQ]VTXW\WR\[FC NM:i:0 CS:Z:T3032301231212301013112222111210000 CQ:Z:7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -1831_577_322 16 phiX 457 255 35M * 0 0 CTTCTGCCGTTTTGGATTTAACCGAAGATGATTTC /E?@MNMJTZM79LI;A5:H@IIHIFLPEDHQXWU NM:i:1 CS:Z:G2003213220230103303201000130312202 CQ:Z:9=;>4506;255464-<#7+194&2<?65968)7/ -1831_577_362 0 phiX 2152 255 35M * 0 0 ACTTATTCGCCACCATGATTATGACCAGTGTTTCC GS`XY^^[ZWMLTH>LEDHI?,3EQDAQPB5%(@6 NM:i:1 CS:Z:A1203302330110131230331210121110220 CQ:Z:62B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -1831_577_382 16 phiX 4685 255 35M * 0 0 GGGTCGCAAGGCTAATGATTCACACGCCGACTGCT *>C@NMMI2333IUD=>FNE;1=LSE19JHEKMJB NM:i:0 CS:Z:A2312123033111120321303230201332100 CQ:Z:12957/:1))=76(*24;,3+:<.&.&-=1=2/5* -1831_577_488 16 phiX 4947 255 35M * 0 0 TGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGC @SEJPW]VUWXQLSPSOMXXXTVZQKJJSG59EKM NM:i:0 CS:Z:G3200302330322110200323132101120301 CQ:Z::48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -1831_577_545 0 phiX 1710 255 35M * 0 0 TTGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT [YWTWZY\_\OKHP[[WTY\VLDDFLTMBBMPOD- NM:i:0 CS:Z:T0112131333222303222210031322103233 CQ:Z:>><<9?<>?A<481@<@8==@76/61<95.5988- -1831_577_637 0 phiX 4246 255 35M * 0 0 CTGTTACTGAGAAGTTAATGGATGAATTGGCACAA D8?2<WFB@DQC1-<OMOLMTSRM=6?G>,EYN?, NM:i:1 CS:Z:C2113312122202103031023120301031110 CQ:Z:8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -1831_577_692 0 phiX 3904 255 35M * 0 0 TGTCTAGGAAATAACCGTCAGGATTGACACCCTCC aMK^^aIG`_^JJ_]]JI[Z]FCX[[XXTU[UKP< NM:i:0 CS:Z:T1122320200330103121202301211100220 CQ:Z:@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< +1831_573_1219 16 phiX174 2201 255 35M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC -A@EE>NVA7FQZSC8GRJK<EVGC<==39BP\__ NM:i:0 CS:Z:G1211130300300301021212330201121310 CQ:Z:@@@=4/+)5)408?'665>*/5?<61';<3,:,5- +1831_573_1242 0 phiX174 647 255 35M * 0 0 TCATCCCGTCAACATTCAAACGGCCTGTCTCATCA [[WSWNGS]US^_\WQW]WL?CEMUIMSTSJ*1U; NM:i:1 CS:Z:T2132003121011302100130302112221121 CQ:Z:>>>::>17=A5?@@=;7A=;2.60>82<8=74+;; +1831_573_1647 16 phiX174 1117 255 35M * 0 0 CGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC 4NIKVOPIBACPWOQ^^WSZ_\Y][Y]]^_[[_^[ NM:i:0 CS:Z:G0222233301013033120132223202022123 CQ:Z:=?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 +1831_573_1684 16 phiX174 3695 255 35M * 0 0 TAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGC ?\VWTLTTUZVV[_^\Y[_ZWUW]^_XKR[SQJNT NM:i:0 CS:Z:G3310013212312012302121010221231123 CQ:Z:7>1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? +1831_574_109 0 phiX174 3728 255 35M * 0 0 GCAGAATCAGCGGTATGGCTCTTCTCATATTGGCG 07651#4817>@65<2:84716=788<1995.7?6 NM:i:1 CS:Z:G3122332123301331032220222133301033 CQ:Z:07651#4817>@65<2:84716=788<1995.7?6 +1831_574_148 16 phiX174 2368 255 35M * 0 0 GTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCA ;NEGQTTTJAMH9B@@PHHSQUJML=LPMUMPJGV NM:i:0 CS:Z:T1200113123030012202302312200010231 CQ:Z:<;->3;;3>//>0;;7=,=4-4/+>029<9<624; +1831_574_575 16 phiX174 4005 255 35M * 0 0 GAATGTCACGCTGATTATTTTGACTTTGAGCGTAT <JC>=PXK;2BW[T;CXA"&?U\\__WU]^[Z]^U NM:i:1 CS:Z:A3313322100212102033032123311211302 CQ:Z:7?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< +1831_574_592 16 phiX174 2949 255 35M * 0 0 GGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCAT 2BBLI?LTSPIFFIMD:?MRLECQ][G7DI9=A?I NM:i:0 CS:Z:A3103330110123102223122023103310330 CQ:Z:73-5)19,,<@>4067<2.-864346;9<1/;212 +1831_574_824 16 phiX174 3996 255 35M * 0 0 TACCCTTCTGAATGTCACGCTGATTATTTTGACTT ?VRCD\ZK5?ZWJ7D]WP=AVQRHH[J64CUZ__Z NM:i:0 CS:Z:A0212100033032123311211302122020013 CQ:Z:;@@@;;),+@<-<7;<&89??&29?<$2:A<);8? +1831_574_1194 0 phiX174 1135 255 35M * 0 0 CGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTC NRXFJ]WXXX^^PP_\\RO\]]SR^_XLRUKC:A6 NM:i:0 CS:Z:C3303101033322220312200222013013312 CQ:Z::5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 +1831_574_1591 16 phiX174 5117 255 35M * 0 0 GAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCG 9CB??UTRA!7YIJXQUSUEEZWX[WNV^ZY^\XY NM:i:1 CS:Z:C3202101330322130221230222201123202 CQ:Z:==<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 +1831_574_1624 16 phiX174 4057 255 35M * 0 0 CTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAA )5?C6:LSC5DHJA6@FNI54;D?137CB3-3CQ: NM:i:1 CS:Z:C0122200222132200313011102302210332 CQ:Z:#<6.&(,7-+))7..'/;43.)927.(<85&13-) +1831_574_1903 0 phiX174 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC TMJT^]XQV__WQY]UUYXUVVV]QNSGOOJOPI/ NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:<956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ +1831_575_54 16 phiX174 3586 255 35M * 0 0 TTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGC 8ST4/MPK:7HONA7BTVCHY[^YRSVLMSMU_\Z NM:i:1 CS:Z:G3331330322230200102132110132013200 CQ:Z:>=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 +1831_575_197 16 phiX174 4860 255 35M * 0 0 AGCTTGCAAAATACGTGGCCTTATGGTTACAGTAT ,=.<SADLUZH>67?JXRIFRTTVOQZ`RHIRXF8 NM:i:1 CS:Z:A3312113010133020301131330001310032 CQ:Z:,-:?463@A:88?6?437<=.2&1.;@67.4@%2, +1831_575_444 16 phiX174 5097 255 35M * 0 0 AAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAAT >XO0/QUSCCY]]LJWZ^[W\ZVGF[^[JIVZ_QM NM:i:1 CS:Z:A3022120112320220100202132332113320 CQ:Z:<2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> +1831_575_622 0 phiX174 2484 255 35M * 0 0 TGTTTTACAGACACCTAAAGCTACATCGTCAACGT `XY^\_^Z[^ZY[Z[WNQOLO?DOBJB@M>EQ$!+ NM:i:1 CS:Z:T1100031122111023002323113231210111 CQ:Z:@A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ +1831_575_938 16 phiX174 1132 255 35M * 0 0 GGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGC 7N@<NSTMKOQVHAONKTXVTUWZXRTWZ^XY_YT NM:i:0 CS:Z:G3103102220022130222233301013033120 CQ:Z:;:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 +1831_575_970 16 phiX174 231 255 35M * 0 0 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCG 5PXYYNKY^\[VW[\]XY[VUTRY_[Y]_ZW\\\\ NM:i:0 CS:Z:C3201311301023133303023011202220221 CQ:Z:=@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 +1831_575_1138 0 phiX174 1912 255 35M * 0 0 CGCTAAAGGTGCTTTGACTTATACCGATATTGCTG XLJ7-IKH@IWNTJJSPUKO]UU[UTNQKDQDCJ1 NM:i:1 CS:Z:C3320002011320012120333103233301321 CQ:Z:<=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 +1831_575_1180 0 phiX174 4168 255 35M * 0 0 AGGGCGTTGAGTTCGATAATGGTGATATGTATGTT J]_RSE@HENVYKKOINRQOV_]VLPSRLHMBJT7 NM:i:0 CS:Z:A2003310122102323303101123331133110 CQ:Z:/<B>5?':/78?;1;55:997@@>94=7<186->7 +1831_575_1302 16 phiX174 5201 255 35M * 0 0 ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCA *57==/2(a)B6+-8?,!,.(.A=+*7>2,841LOB6 NM:i:1 CS:Z:T1201303312333123130200123201013021 CQ:Z:&12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* +1831_575_1310 16 phiX174 1611 255 35M * 0 0 ATACTGACCAAGAACGTGATTACTTCATGCAGCGT ;QC!!DXV[[Z]UEN_YYPAMSVGGXQWQHKSYWQ NM:i:1 CS:Z:A1332131312021303211310220101211133 CQ:Z:6<<>663?99@(@7=11@:@@/7??<@<;>'3-7; +1831_575_1321 0 phiX174 2663 255 35M * 0 0 GTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACT 0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 NM:i:1 CS:Z:G1001010233200122122022023000203212 CQ:Z:0;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 +1831_575_1373 16 phiX174 4220 255 35M * 0 0 TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTG <M=?PSE>BHTUGKZZZYY]]VU]^[TUWZ]]__` NM:i:0 CS:Z:C1213011223311001221321132013121220 CQ:Z:A@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< +1831_575_1436 0 phiX174 3459 255 35M * 0 0 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATAC ;Q\WMKB<NE=OUWRFO[V?=PUXC6LZN77CHQ< NM:i:0 CS:Z:G3210313021212303321202113301220331 CQ:Z:*2@=;39*3<*4<:>52>>9'7:<='0=>1'136< +1831_575_1442 0 phiX174 3316 255 35M * 0 0 ATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT URLSZUTH;RWB;GTWUNS\^ZJP^SGKFMSB?N> NM:i:0 CS:Z:A3132010022331132101132123132020222 CQ:Z:8>58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> +1831_575_1500 16 phiX174 4268 255 35M * 0 0 TGAATTGGCACAATGCTACAATGTGCTCCCCCAAC 9V\UBGWPPNT^YUQQQQUQLPRUQQSV^`_^_^P NM:i:0 CS:Z:G1010000223111301132313011130103021 CQ:Z:2?@@?A@?8<6<:985=99999==B3<5<<,7?>9 +1831_575_1535 16 phiX174 1224 255 35M * 0 0 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATG <PRXVWQOTQUST^[\WMT^]Z\_`ZX`a_[[\^a NM:i:0 CS:Z:C1312012030320112110211013300131121 CQ:Z:@B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< +1831_576_86 16 phiX174 2980 255 35M * 0 0 CCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCC /@:AJ7;AEH712=EJKF>=LHJP?587CK:9AHN NM:i:0 CS:Z:G0320000121033022010011030032211310 CQ:Z:7811)2:*.++5</:3+43924*))/:,6&29)2/ +1831_576_266 16 phiX174 279 255 35M * 0 0 TAGATATGAGTCACATTTTGTTCATGGTAGAGATT 6;*<NGC9=TWH2<P=+#.P]IDV]\SUZVW[^_[ NM:i:1 CS:Z:A0322223101312011300311121221333223 CQ:Z:<@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 +1831_576_327 16 phiX174 4516 255 35M * 0 0 TTACTATTCAGCGTTTGATGAATGCAATGCGACAG =RQYVTNGR]_RNXYVYROYZ][Y\^[VZ_UU^^[ NM:i:0 CS:Z:C2112331301313021321001332120332130 CQ:Z:<@?@6@@;<@?><@>==3@:==<3@@>53<9><6= +1831_576_519 16 phiX174 1624 255 35M * 0 0 ACGTGATTACTTCATGCAGCGTTACCGTGATGTTA 7ACFAB?LF;BBIVNHOXTOMLYTD@O]VOTQIPY NM:i:0 CS:Z:T3011321130130133213131202130321131 CQ:Z:==46<97@>2/6?;2<4A881>9121+<1/4.9+7 +1831_576_603 16 phiX174 1575 255 35M * 0 0 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTG 8PMKX]PIR\`ZJO]_[HGZ_XOW\Z]LPb\RIS_ NM:i:0 CS:Z:C1003032313302312320131221001330311 CQ:Z:@@46=@C.??<A79@@;-<@@>29B?>55<B7598 +1831_576_655 16 phiX174 3291 255 35M * 0 0 CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGA %06ESGLVW^JATXW73V][JCT_]G?Q[_XYa`\ NM:i:1 CS:Z:T2001023130302322122200313123123102 CQ:Z:=@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% +1831_576_815 0 phiX174 5185 255 35M * 0 0 CGGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC NP]^WV]^`^ZZWX^_]][ZWKFQPA?FSTQPKD. NM:i:0 CS:Z:C3022113203032010120310102321001031 CQ:Z:<3>@?9>@?B=>=;>A???=>:25=4.25?6<57. +1831_576_882 0 phiX174 5052 255 35M * 0 0 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTC PGTVV^YMQ]]VNT]ZWXQ;7LYVPKIRXTTLNU8 NM:i:0 CS:Z:G3230020122320223230022031020110122 CQ:Z:?26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 +1831_576_898 0 phiX174 517 255 35M * 0 0 GGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGC \_bTPa`\ZY]WOMW`YYLL]VNS^]SSLES][J. NM:i:0 CS:Z:G0230132312121033222231132231233213 CQ:Z:=@@C2?C>?<>@886B?;?.??87=B<8<15??=. +1831_576_923 0 phiX174 1049 255 35M * 0 0 CATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCT LCBEMWHCNQTTNSXUNLTVUKAKV[TMRRURIJ7 NM:i:0 CS:Z:C1322010320202013210121223010123122 CQ:Z:76.51=;.699<96>;;49<;;11;<@59:9=647 +1831_576_1131 16 phiX174 4060 255 35M * 0 0 TTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCC <MJBDSMK>BWZI2FPGKEOI<PWVQ?KNN>>SC@ NM:i:1 CS:Z:G0233122200222132200313011102302210 CQ:Z:104@#@/@,4>9?2+?1571@',>=;(759;*92< +1831_576_1289 16 phiX174 1898 255 35M * 0 0 ATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTA 0DBK[ONJ9GWSQ@;@CINYOHKU_VQZ_aRNYTX NM:i:0 CS:Z:T3021210023110200323310302013121203 CQ:Z:@9<>1B@@;7@@663==28,5':8<<,.=2>>.50 +1831_576_1367 0 phiX174 1838 255 35M * 0 0 GAGCATGGCACTATGTTTACTCTTGCGCTTGTTCG ]^_[Y]_\\[[[X\]]^]WRXZXZZXSROMXVNN7 NM:i:0 CS:Z:G2231310311233110031222013332011023 CQ:Z:??@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 +1831_576_1416 0 phiX174 4521 255 35M * 0 0 ATTCAGCGTTTGATGAATGCAATGCGACAGGCTCA 1AYL;>>I[F4JG@CBSURK<KUQB,AZRJCFPW@ NM:i:0 CS:Z:A3021233100123120313103133211203221 CQ:Z:+';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ +1831_576_1605 0 phiX174 5208 255 35M * 0 0 AAGCTGGGTTACGACGCGACGCCGTTCAACCAGAC Q[bb_]NKZYTVW[_XX^]]WTNQSA>BMPKNMB, NM:i:1 CS:Z:A0232100103132133321330310210101221 CQ:Z:6<@C@@>1;@:;<<@@9@???9<3?5-21=4877, +1831_576_1729 16 phiX174 5193 255 35M * 0 0 TTAATCCAACTTACCAAGCTGGGTTACGACGCGAC >ZL:FYXSQV]^ZSW^\TU\\[YKM_^][ZZZ^^^ NM:i:0 CS:Z:G1233312313010012320101302101023030 CQ:Z:@?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> +1831_576_1982 16 phiX174 5023 255 35M * 0 0 TTAACAAAAAGTCAGATATGGACCTTGCTGCTAAA @JFRDK\_\MQUU_UQST^ZX^[\XX[Y^LK^^_K NM:i:0 CS:Z:T0032312310201201333221212000011030 CQ:Z:,@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ +1831_577_133 16 phiX174 1713 255 35M * 0 0 TCATGCGCTCTAATCTCTGGGCATCTGGCTATGAT )&/8<NA=EPP;FEI]YY]_VFO]HDXOM[\[]SB NM:i:1 CS:Z:A3213323012231300122223032223331322 CQ:Z:/4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) +1831_577_281 16 phiX174 4576 255 35M * 0 0 TTTTTGACACTCTCACGTTGGCTGACGACCGATTA ?XWE?WXSYURPOYWMJ@I[[RQ]VTXW\WR\[FC NM:i:0 CS:Z:T3032301231212301013112222111210000 CQ:Z:7-:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? +1831_577_322 16 phiX174 457 255 35M * 0 0 CTTCTGCCGTTTTGGATTTAACCGAAGATGATTTC /E?@MNMJTZM79LI;A5:H@IIHIFLPEDHQXWU NM:i:1 CS:Z:G2003213220230103303201000130312202 CQ:Z:9=;>4506;255464-<#7+194&2<?65968)7/ +1831_577_362 0 phiX174 2152 255 35M * 0 0 ACTTATTCGCCACCATGATTATGACCAGTGTTTCC GS`XY^^[ZWMLTH>LEDHI?,3EQDAQPB5%(@6 NM:i:1 CS:Z:A1203302330110131230331210121110220 CQ:Z:62B?:@?@<?958=,3:,90:&'-99,6<5.($+6 +1831_577_382 16 phiX174 4685 255 35M * 0 0 GGGTCGCAAGGCTAATGATTCACACGCCGACTGCT *>C@NMMI2333IUD=>FNE;1=LSE19JHEKMJB NM:i:0 CS:Z:A2312123033111120321303230201332100 CQ:Z:12957/:1))=76(*24;,3+:<.&.&-=1=2/5* +1831_577_488 16 phiX174 4947 255 35M * 0 0 TGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGC @SEJPW]VUWXQLSPSOMXXXTVZQKJJSG59EKM NM:i:0 CS:Z:G3200302330322110200323132101120301 CQ:Z::48.,*>6566<?8=<=<2>6;94>;=9>@8924@ +1831_577_545 0 phiX174 1710 255 35M * 0 0 TTGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT [YWTWZY\_\OKHP[[WTY\VLDDFLTMBBMPOD- NM:i:0 CS:Z:T0112131333222303222210031322103233 CQ:Z:>><<9?<>?A<481@<@8==@76/61<95.5988- +1831_577_637 0 phiX174 4246 255 35M * 0 0 CTGTTACTGAGAAGTTAATGGATGAATTGGCACAA D8?2<WFB@DQC1-<OMOLMTSRM=6?G>,EYN?, NM:i:1 CS:Z:C2113312122202103031023120301031110 CQ:Z:8-,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, +1831_577_692 0 phiX174 3904 255 35M * 0 0 TGTCTAGGAAATAACCGTCAGGATTGACACCCTCC aMK^^aIG`_^JJ_]]JI[Z]FCX[[XXTU[UKP< NM:i:0 CS:Z:T1122320200330103121202301211100220 CQ:Z:@B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< --- a/tool-data/bowtie_indices.loc.sample +++ b/tool-data/bowtie_indices.loc.sample @@ -1,29 +1,37 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie indexed sequences data files. You will need -#to create these data files and then create a bowtie_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bowtie_indices.loc -#file has this format (white space characters are TAB characters): +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 gh18.3.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt #...etc... # -#Your bowtie_indices.loc file should include an entry per line for -#each index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/test-data/bwa_wrapper_out3.sam +++ b/test-data/bwa_wrapper_out3.sam @@ -1,60 +1,60 @@ -seq1 113 phiX 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq1 177 phiX 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -seq10 129 phiX 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq10 65 phiX 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 -seq11 129 phiX 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq11 65 phiX 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 -seq12 129 phiX 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 -seq12 65 phiX 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq13 129 phiX 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 -seq13 65 phiX 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 -seq14 129 phiX 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 -seq14 65 phiX 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 -seq15 129 phiX 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 -seq15 65 phiX 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 -seq16 129 phiX 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq16 65 phiX 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 -seq17 129 phiX 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 -seq17 65 phiX 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq18 133 phiX 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII -seq18 73 phiX 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 -seq19 129 phiX 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq19 65 phiX 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq2 129 phiX 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq2 65 phiX 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 129 phiX 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 65 phiX 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq21 129 phiX 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq21 65 phiX 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 -seq22 137 phiX 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq22 69 phiX 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII -seq23 129 phiX 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 -seq23 65 phiX 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 -seq24 129 phiX 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq24 65 phiX 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq25 129 phiX 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 -seq25 65 phiX 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 -seq26 129 phiX 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq26 65 phiX 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq27 129 phiX 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 -seq27 65 phiX 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 -seq28 129 phiX 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq28 65 phiX 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 -seq29 133 phiX 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII -seq29 73 phiX 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 -seq3 129 phiX 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq3 65 phiX 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq30 129 phiX 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 -seq30 65 phiX 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq4 137 phiX 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 -seq4 69 phiX 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII -seq5 129 phiX 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 -seq5 65 phiX 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 -seq6 129 phiX 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq6 65 phiX 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 -seq7 129 phiX 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq7 65 phiX 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 -seq8 137 phiX 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq8 69 phiX 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII -seq9 129 phiX 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq9 65 phiX 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 +seq1 113 phiX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq1 177 phiX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +seq10 129 phiX174 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq10 65 phiX174 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 +seq11 129 phiX174 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq11 65 phiX174 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 +seq12 129 phiX174 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 +seq12 65 phiX174 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq13 129 phiX174 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 +seq13 65 phiX174 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 +seq14 129 phiX174 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 +seq14 65 phiX174 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 +seq15 129 phiX174 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 +seq15 65 phiX174 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 +seq16 129 phiX174 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq16 65 phiX174 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 +seq17 129 phiX174 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 +seq17 65 phiX174 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq18 133 phiX174 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII +seq18 73 phiX174 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 +seq19 129 phiX174 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq19 65 phiX174 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq2 129 phiX174 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq2 65 phiX174 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 129 phiX174 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 65 phiX174 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq21 129 phiX174 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq21 65 phiX174 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 +seq22 137 phiX174 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq22 69 phiX174 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII +seq23 129 phiX174 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 +seq23 65 phiX174 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 +seq24 129 phiX174 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq24 65 phiX174 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq25 129 phiX174 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 +seq25 65 phiX174 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 +seq26 129 phiX174 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq26 65 phiX174 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq27 129 phiX174 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 +seq27 65 phiX174 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 +seq28 129 phiX174 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq28 65 phiX174 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 +seq29 133 phiX174 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII +seq29 73 phiX174 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 +seq3 129 phiX174 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq3 65 phiX174 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq30 129 phiX174 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 +seq30 65 phiX174 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq4 137 phiX174 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 +seq4 69 phiX174 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII +seq5 129 phiX174 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 +seq5 65 phiX174 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 +seq6 129 phiX174 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq6 65 phiX174 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 +seq7 129 phiX174 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq7 65 phiX174 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 +seq8 137 phiX174 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq8 69 phiX174 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII +seq9 129 phiX174 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq9 65 phiX174 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of BWA indexed sequences data files. You will need -#to create these data files and then create a bwa_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bwa_index.loc -#file has this format (white space characters are TAB characters): +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/base/, #then the bwa_index.loc entry would look like this: # -#phiX /depot/data2/galaxy/phiX/base/phiX.fa +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa # #and your /depot/data2/galaxy/phiX/base/ directory #would contain phiX.fa.* files: @@ -22,8 +22,17 @@ #...etc... # #Your bwa_index.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually +#index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX /depot/data2/galaxy/phiX/base/phiX.fa -#hg18 /depot/data2/galaxy/hg18/base/hg18.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.5"><description>Search translated nucleotide database with protein query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ tblastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/sr_mapping/lastz_paired_reads_wrapper.py +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.py @@ -758,7 +758,7 @@ def __main__(): parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' ) ( options, args ) = parser.parse_args() - if options.ref_name != 'None': + if options.ref_name: ref_name = '[nickname=%s]' % options.ref_name else: ref_name = '' --- a/tools/sr_mapping/bowtie_wrapper.py +++ b/tools/sr_mapping/bowtie_wrapper.py @@ -137,51 +137,51 @@ def __main__(): indexing_cmds = '%s' % colorspace else: try: - if options.iautoB != 'None' and options.iautoB == 'set': + if options.iautoB and options.iautoB == 'set': iautoB = '--noauto' else: iautoB = '' - if options. ipacked != 'None' and options.ipacked == 'packed': + if options. ipacked and options.ipacked == 'packed': ipacked = '--packed' else: ipacked = '' - if options.ibmax != 'None' and int( options.ibmax ) >= 1: + if options.ibmax and int( options.ibmax ) >= 1: ibmax = '--bmax %s' % options.ibmax else: ibmax = '' - if options.ibmaxdivn != 'None' and int( options.ibmaxdivn ) >= 0: + if options.ibmaxdivn and int( options.ibmaxdivn ) >= 0: ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn else: ibmaxdivn = '' - if options.idcv != 'None' and int( options.idcv ) > 0: + if options.idcv and int( options.idcv ) > 0: idcv = '--dcv %s' % options.idcv else: idcv = '' - if options.inodc != 'None' and options.inodc == 'nodc': + if options.inodc and options.inodc == 'nodc': inodc = '--nodc' else: inodc = '' - if options.inoref != 'None' and options.inoref == 'noref': + if options.inoref and options.inoref == 'noref': inoref = '--noref' else: inoref = '' - if options.iftab != 'None' and int( options.iftab ) >= 0: + if options.iftab and int( options.iftab ) >= 0: iftab = '--ftabchars %s' % options.iftab else: iftab = '' - if options.intoa != 'None' and options.intoa == 'yes': + if options.intoa and options.intoa == 'yes': intoa = '--ntoa' else: intoa = '' - if options.iendian != 'None' and options.iendian == 'big': + if options.iendian and options.iendian == 'big': iendian = '--big' else: iendian = '--little' - if options.iseed != 'None' and int( options.iseed ) > 0: + if options.iseed and int( options.iseed ) > 0: iseed = '--seed %s' % options.iseed else: iseed = '' - if options.icutoff != 'None' and int( options.icutoff ) > 0: + if options.icutoff and int( options.icutoff ) > 0: icutoff = '--cutoff %s' % options.icutoff else: icutoff = '' @@ -233,11 +233,11 @@ def __main__(): suppressHeader = '--sam-nohead' else: suppressHeader = '' - if options.maxInsert != 'None' and int( options.maxInsert ) > 0: + if options.maxInsert and int( options.maxInsert ) > 0: maxInsert = '-X %s' % options.maxInsert else: maxInsert = '' - if options.mateOrient != 'None': + if options.mateOrient: mateOrient = '--%s' % options.mateOrient else: mateOrient = '' @@ -246,32 +246,32 @@ def __main__(): ( maxInsert, mateOrient, options.threads, suppressHeader, colorspace ) else: try: - if options.skip != 'None' and int( options.skip ) > 0: + if options.skip and int( options.skip ) > 0: skip = '-s %s' % options.skip else: skip = '' - if options.alignLimit != 'None' and int( options.alignLimit ) >= 0: + if options.alignLimit and int( options.alignLimit ) >= 0: alignLimit = '-u %s' % options.alignLimit else: alignLimit = '' - if options.trimH != 'None' and int( options.trimH ) > 0: + if options.trimH and int( options.trimH ) > 0: trimH = '-5 %s' % options.trimH else: trimH = '' - if options.trimL != 'None' and int( options.trimL ) > 0: + if options.trimL and int( options.trimL ) > 0: trimL = '-3 %s' % options.trimL else: trimL = '' - if options.mismatchSeed != 'None' and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ + if options.mismatchSeed and (options.mismatchSeed == '0' or options.mismatchSeed == '1' \ or options.mismatchSeed == '2' or options.mismatchSeed == '3'): mismatchSeed = '-n %s' % options.mismatchSeed else: mismatchSeed = '' - if options.mismatchQual != 'None' and int( options.mismatchQual ) >= 0: + if options.mismatchQual and int( options.mismatchQual ) >= 0: mismatchQual = '-e %s' % options.mismatchQual else: mismatchQual = '' - if options.seedLen != 'None' and int( options.seedLen ) >= 5: + if options.seedLen and int( options.seedLen ) >= 5: seedLen = '-l %s' % options.seedLen else: seedLen = '' @@ -283,11 +283,11 @@ def __main__(): maqSoapAlign = '-v %s' % options.maqSoapAlign else: maqSoapAlign = '' - if options.minInsert != 'None' and int( options.minInsert ) > 0: + if options.minInsert and int( options.minInsert ) > 0: minInsert = '-I %s' % options.minInsert else: minInsert = '' - if options.maxAlignAttempt != 'None' and int( options.maxAlignAttempt ) >= 0: + if options.maxAlignAttempt and int( options.maxAlignAttempt ) >= 0: maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt else: maxAlignAttempt = '' @@ -299,7 +299,7 @@ def __main__(): reverseAlign = '--norc' else: reverseAlign = '' - if options.maxBacktracks != 'None' and int( options.maxBacktracks ) > 0 and \ + if options.maxBacktracks and int( options.maxBacktracks ) > 0 and \ ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ): maxBacktracks = '--maxbts %s' % options.maxBacktracks else: @@ -308,7 +308,7 @@ def __main__(): tryHard = '-y' else: tryHard = '' - if options.valAlign != 'None' and int( options.valAlign ) >= 0: + if options.valAlign and int( options.valAlign ) >= 0: valAlign = '-k %s' % options.valAlign else: valAlign = '' @@ -316,7 +316,7 @@ def __main__(): allValAligns = '-a' else: allValAligns = '' - if options.suppressAlign != 'None' and int( options.suppressAlign ) >= 0: + if options.suppressAlign and int( options.suppressAlign ) >= 0: suppressAlign = '-m %s' % options.suppressAlign else: suppressAlign = '' @@ -328,23 +328,23 @@ def __main__(): strata = '--strata' else: strata = '' - if options.offrate != 'None' and int( options.offrate ) >= 0: + if options.offrate and int( options.offrate ) >= 0: offrate = '-o %s' % options.offrate else: offrate = '' - if options.seed != 'None' and int( options.seed ) >= 0: + if options.seed and int( options.seed ) >= 0: seed = '--seed %s' % options.seed else: seed = '' - if options.snpphred != 'None' and int( options.snpphred ) >= 0: + if options.snpphred and int( options.snpphred ) >= 0: snpphred = '--snpphred %s' % options.snpphred else: snpphred = '' - if options.snpfrac != 'None' and float( options.snpfrac ) >= 0: + if options.snpfrac and float( options.snpfrac ) >= 0: snpfrac = '--snpfrac %s' % options.snpfrac else: snpfrac = '' - if options.keepends != 'None' and options.keepends == 'doKeepends': + if options.keepends and options.keepends == 'doKeepends': keepends = '--col-keepends' else: keepends = '' --- a/test-data/megablast_wrapper_test1.out +++ b/test-data/megablast_wrapper_test1.out @@ -1,20 +1,20 @@ -0_0.666667 PHIX174 100.00 30 0 0 1 30 1 30 1e-13 60.0 -1_0.600000 PHIX174 100.00 30 0 0 1 30 31 60 1e-13 60.0 -2_0.400000 PHIX174 100.00 30 0 0 1 30 76 105 1e-13 60.0 -3_0.566667 PHIX174 100.00 30 0 0 1 30 106 135 1e-13 60.0 -4_0.766667 PHIX174 100.00 30 0 0 1 30 151 180 1e-13 60.0 -5_0.533333 PHIX174 100.00 30 0 0 1 30 181 210 1e-13 60.0 -6_0.533333 PHIX174 100.00 30 0 0 1 30 226 255 1e-13 60.0 -7_0.400000 PHIX174 100.00 30 0 0 1 30 256 285 1e-13 60.0 -8_0.500000 PHIX174 100.00 30 0 0 1 30 301 330 1e-13 60.0 -9_0.400000 PHIX174 100.00 30 0 0 1 30 331 360 1e-13 60.0 -10_0.500000 PHIX174 100.00 30 0 0 1 30 376 405 1e-13 60.0 -11_0.533333 PHIX174 100.00 30 0 0 1 30 406 435 1e-13 60.0 -12_0.700000 PHIX174 100.00 30 0 0 1 30 451 480 1e-13 60.0 -13_0.533333 PHIX174 100.00 30 0 0 1 30 481 510 1e-13 60.0 -14_0.666667 PHIX174 100.00 30 0 0 1 30 526 555 1e-13 60.0 -15_0.666667 PHIX174 100.00 30 0 0 1 30 556 585 1e-13 60.0 -16_0.566667 PHIX174 100.00 30 0 0 1 30 601 630 1e-13 60.0 -17_0.533333 PHIX174 100.00 30 0 0 1 30 631 660 1e-13 60.0 -18_0.566667 PHIX174 100.00 30 0 0 1 30 676 705 1e-13 60.0 -19_0.566667 PHIX174 100.00 30 0 0 1 30 706 735 1e-13 60.0 +0_0.666667 phiX174 5386 100.00 30 0 0 1 30 1 30 1e-13 60.0 +1_0.600000 phiX174 5386 100.00 30 0 0 1 30 31 60 1e-13 60.0 +2_0.400000 phiX174 5386 100.00 30 0 0 1 30 76 105 1e-13 60.0 +3_0.566667 phiX174 5386 100.00 30 0 0 1 30 106 135 1e-13 60.0 +4_0.766667 phiX174 5386 100.00 30 0 0 1 30 151 180 1e-13 60.0 +5_0.533333 phiX174 5386 100.00 30 0 0 1 30 181 210 1e-13 60.0 +6_0.533333 phiX174 5386 100.00 30 0 0 1 30 226 255 1e-13 60.0 +7_0.400000 phiX174 5386 100.00 30 0 0 1 30 256 285 1e-13 60.0 +8_0.500000 phiX174 5386 100.00 30 0 0 1 30 301 330 1e-13 60.0 +9_0.400000 phiX174 5386 100.00 30 0 0 1 30 331 360 1e-13 60.0 +10_0.500000 phiX174 5386 100.00 30 0 0 1 30 376 405 1e-13 60.0 +11_0.533333 phiX174 5386 100.00 30 0 0 1 30 406 435 1e-13 60.0 +12_0.700000 phiX174 5386 100.00 30 0 0 1 30 451 480 1e-13 60.0 +13_0.533333 phiX174 5386 100.00 30 0 0 1 30 481 510 1e-13 60.0 +14_0.666667 phiX174 5386 100.00 30 0 0 1 30 526 555 1e-13 60.0 +15_0.666667 phiX174 5386 100.00 30 0 0 1 30 556 585 1e-13 60.0 +16_0.566667 phiX174 5386 100.00 30 0 0 1 30 601 630 1e-13 60.0 +17_0.533333 phiX174 5386 100.00 30 0 0 1 30 631 660 1e-13 60.0 +18_0.566667 phiX174 5386 100.00 30 0 0 1 30 676 705 1e-13 60.0 +19_0.566667 phiX174 5386 100.00 30 0 0 1 30 706 735 1e-13 60.0 --- a/tools/sr_mapping/srma_wrapper.xml +++ b/tools/sr_mapping/srma_wrapper.xml @@ -1,17 +1,28 @@ -<tool id="srma_wrapper" name="Re-align with SRMA" version="0.1.5"> +<tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.0"><description></description><command interpreter="python">srma_wrapper.py #if $refGenomeSource.refGenomeSource_type == "history": - --ref=$refGenomeSource.ownFile + --ref=$refGenomeSource.ownFile #else: - --refUID=$refGenomeSource.ref - --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }" + --refUID=$refGenomeSource.ref + --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc #end if - --input=$input --inputIndex=${input.metadata.bam_index} --output=$output - --params=$params.source_select --fileSource=$refGenomeSource.refGenomeSource_type + --input=$input + --inputIndex=${input.metadata.bam_index} + --output=$output + --params=$params.source_select + --fileSource=$refGenomeSource.refGenomeSource_type --jarBin="${GALAXY_DATA_INDEX_DIR}/shared/jars" #if $params.source_select == "full": - --offset=$params.offset --minMappingQuality=$params.minMappingQuality --minAlleleProbability=$params.minAlleleProbability --minAlleleCoverage=$params.minAlleleCoverage --range=$params.range --correctBases=$params.correctBases --useSequenceQualities=$params.useSequenceQualities --maxHeapSize=$params.maxHeapSize + --offset=$params.offset + --minMappingQuality=$params.minMappingQuality + --minAlleleProbability=$params.minAlleleProbability + --minAlleleCoverage=$params.minAlleleCoverage + --range=$params.range + --correctBases=$params.correctBases + --useSequenceQualities=$params.useSequenceQualities + --maxHeapSize=$params.maxHeapSize #end if --jarFile="srma.jar" </command> @@ -23,10 +34,7 @@ </param><when value="built-in"><param name="ref" type="select" label="Select a reference genome"> - <options from_file="srma_index.loc"> - <column name="value" index="0" /> - <column name="name" index="0" /> - </options> + <options from_data_table="srma_indexes" /></param></when><when value="history"> @@ -71,13 +79,13 @@ <tests><test><param name="refGenomeSource_type" value="built-in" /><param name="ref" value="hg18chr21" /> @@ -87,16 +95,16 @@ </test><test><param name="refGenomeSource_type" value="history" /><param name="ownFile" value="srma_in2.fa" /> --- a/tools/sr_mapping/bwa_wrapper.py +++ b/tools/sr_mapping/bwa_wrapper.py @@ -30,8 +30,9 @@ usage: bwa_wrapper.py [options] -T, --outputTopN=T: Output top specified hits -S, --maxInsertSize=S: Maximum insert size for a read pair to be considered mapped good -P, --maxOccurPairing=P: Maximum occurrences of a read for pairings + -H, --suppressHeader=h: Suppress header -D, --dbkey=D: Dbkey for reference genome - -H, --suppressHeader=h: Suppress header + -X, --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is' """ import optparse, os, shutil, subprocess, sys, tempfile @@ -68,13 +69,14 @@ def __main__(): parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' ) parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' ) parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) + parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', help="Don't build index" ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() # make temp directory for placement of indices tmp_index_dir = tempfile.mkdtemp() tmp_dir = tempfile.mkdtemp() # index if necessary - if options.fileSource == 'history': + if options.fileSource == 'history' and not options.do_not_build_index: ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) ref_file_name = ref_file.name ref_file.close() --- a/tools/sr_mapping/srma_wrapper.py +++ b/tools/sr_mapping/srma_wrapper.py @@ -28,6 +28,15 @@ def stop_err( msg ): sys.stderr.write( '%s\n' % msg ) sys.exit() +def parseRefLoc( refLoc, refUID ): + for line in open( refLoc ): + if not line.startswith( '#' ): + fields = line.strip().split( '\t' ) + if len( fields ) >= 3: + if fields[0] == refUID: + return fields[1] + return None + def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -125,13 +134,10 @@ def __main__(): stop_err( 'Problem handling SRMA index (dict file) for custom genome file: %s\n' % str( e ) ) # using built-in dict/index files else: - for line in open( options.refLocations ): - if not line.startswith( '#' ): - fields = line.strip().split( '\t' ) - if len( fields ) >= 2: - if fields[0] == options.refUID: - reference_filepath_name = fields[1] - break + if options.ref: + reference_filepath_name = options.ref + else: + reference_filepath_name = parseRefLoc( options.refLocation, options.refUID ) if reference_filepath_name is None: raise ValueError( 'A valid genome reference was not provided.' ) --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,7 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 /depot/data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 /depot/data/galaxy/hg19/perm_index/hg19_color_F3_50.index +# --- a/test-data/perm_out1.sam +++ b/test-data/perm_out1.sam @@ -1,33 +1,33 @@ -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 65 PHIX174 5 255 50M = 69 64 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 129 PHIX174 69 255 50M = 5 64 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1578:331/1 65 PHIX174 209 255 50M = 268 59 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1578:331/1 129 PHIX174 268 255 50M = 209 59 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 65 PHIX174 401 255 50M = 451 50 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 129 PHIX174 451 255 50M = 401 50 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1570:620/2 0 PHIX174 559 255 50M * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 65 PHIX174 803 255 50M = 868 65 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 129 PHIX174 868 255 50M = 803 65 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1652:270/2 0 PHIX174 973 255 50M * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 PHIX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 PHIX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1598:534/1 65 PHIX174 1717 255 50M = 1772 55 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1598:534/1 129 PHIX174 1772 255 50M = 1717 55 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:324/2 0 PHIX174 1972 255 50M * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 65 PHIX174 2201 255 50M = 2251 50 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 129 PHIX174 2251 255 50M = 2201 50 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 65 PHIX174 2301 255 50M = 2355 54 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 129 PHIX174 2355 255 50M = 2301 54 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 65 PHIX174 2501 255 50M = 2566 65 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 129 PHIX174 2566 255 50M = 2501 65 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1616:363/1 65 PHIX174 2718 255 50M = 2773 55 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1616:363/1 129 PHIX174 2773 255 50M = 2718 55 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 65 PHIX174 3118 255 50M = 3173 55 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 129 PHIX174 3173 255 50M = 3118 55 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 65 PHIX174 3518 255 50M = 3577 59 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 129 PHIX174 3577 255 50M = 3518 59 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 65 PHIX174 3818 255 50M = 3873 55 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 129 PHIX174 3873 255 50M = 3818 55 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 65 PHIX174 4018 255 50M = 4072 54 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 129 PHIX174 4072 255 50M = 4018 54 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 65 PHIX174 4418 255 50M = 4473 55 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 129 PHIX174 4473 255 50M = 4418 55 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 65 phiX174 5 255 50M = 69 64 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 129 phiX174 69 255 50M = 5 64 TTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGG IIIIIII""IIIIIII0II?I""IIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 65 phiX174 209 255 50M = 268 59 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1578:331/1 129 phiX174 268 255 50M = 209 59 AAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 65 phiX174 401 255 50M = 451 50 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 129 phiX174 451 255 50M = 401 50 TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/2 0 phiX174 559 255 50M * 0 0 CTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCT IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 65 phiX174 803 255 50M = 868 65 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 129 phiX174 868 255 50M = 803 65 TTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCA IIIIIII""IIIIIIIIIIIIIIIIIII<III@II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/2 0 phiX174 973 255 50M * 0 0 GCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 65 phiX174 1717 255 50M = 1772 55 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1598:534/1 129 phiX174 1772 255 50M = 1717 55 TTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/2 0 phiX174 1972 255 50M * 0 0 GCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGT IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 65 phiX174 2201 255 50M = 2251 50 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 129 phiX174 2251 255 50M = 2201 50 GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 65 phiX174 2301 255 50M = 2355 54 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1629:446/1 129 phiX174 2355 255 50M = 2301 54 CAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 65 phiX174 2501 255 50M = 2566 65 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 129 phiX174 2566 255 50M = 2501 65 CATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 65 phiX174 2718 255 50M = 2773 55 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1616:363/1 129 phiX174 2773 255 50M = 2718 55 GTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAATGTTTATGTTGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 65 phiX174 3118 255 50M = 3173 55 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 129 phiX174 3173 255 50M = 3118 55 AGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATA IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 65 phiX174 3518 255 50M = 3577 59 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 129 phiX174 3577 255 50M = 3518 59 ACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 65 phiX174 3818 255 50M = 3873 55 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 129 phiX174 3873 255 50M = 3818 55 GACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTC III""""""IIIIIIIII""FI"IIII""II+ICI?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 65 phiX174 4018 255 50M = 4072 54 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 129 phiX174 4072 255 50M = 4018 54 GCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1?I0IIIIHIIIGIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 65 phiX174 4418 255 50M = 4473 55 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 129 phiX174 4473 255 50M = 4418 55 TCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTAT IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II?I0IIIIHIIIGIII NM:i:0 --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.5"><description>Search nucleotide database with nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ blastn </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of 2bit genome files for use with Lastz. You will -#need to supply these files and then create a lastz_seqs.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The lastz_seqs.loc +#to use a directory of 2bit genome files for use with Lastz. You will +#need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<build><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: @@ -22,4 +22,9 @@ # #Your lastz_seqs.loc file should include an entry per line for #each file you have stored that you want to be available. Note that -#your files should all have the extension '2bit'. +#your files should all have the extension '2bit'. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.0.6"> +<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.0"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><command interpreter="python"> @@ -8,186 +8,100 @@ --output=$output --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource - --snpphred="None" - --snpfrac="None" - --keepends="None" #if $refGenomeSource.genomeSource == "history": - #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): - --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" - --do_not_build_index - #else: - --ref=$refGenomeSource.ownFile - --indexSettings=$refGenomeSource.indexParams.indexSettings - #if $refGenomeSource.indexParams.indexSettings == "indexFull": - --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB - #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": - --ipacked=$refGenomeSource.indexParams.autoBehavior.packed - --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax - --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn - --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + ##index already exists + #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): + ##user previously built + --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" + --do_not_build_index #else: - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" + ##build index on the fly + --ref=$refGenomeSource.ownFile + --indexSettings=$refGenomeSource.indexParams.indexSettings + #if $refGenomeSource.indexParams.indexSettings == "indexFull": + --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB + #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": + --ipacked=$refGenomeSource.indexParams.autoBehavior.packed + --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax + --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn + --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + #end if + --inodc=$refGenomeSource.indexParams.nodc + --inoref=$refGenomeSource.indexParams.noref + --ioffrate=$refGenomeSource.indexParams.offrate + --iftab=$refGenomeSource.indexParams.ftab + --intoa=$refGenomeSource.indexParams.ntoa + --iendian=$refGenomeSource.indexParams.endian + --iseed=$refGenomeSource.indexParams.seed + --icutoff=$refGenomeSource.indexParams.cutoff + #end if #end if - --inodc=$refGenomeSource.indexParams.nodc - --inoref=$refGenomeSource.indexParams.noref - --ioffrate=$refGenomeSource.indexParams.offrate - --iftab=$refGenomeSource.indexParams.ftab - --intoa=$refGenomeSource.indexParams.ntoa - --iendian=$refGenomeSource.indexParams.endian - --iseed=$refGenomeSource.indexParams.seed - --icutoff=$refGenomeSource.indexParams.cutoff - #else: - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" - #end if - #end if - #else: - --ref=$refGenomeSource.index - --indexSettings="None" - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" + #else + ##use pre-built index + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": - --input1=$singlePaired.sInput1 - --input2="None" - --params=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --skip=$singlePaired.sParams.sSkip - --alignLimit=$singlePaired.sParams.sAlignLimit - --trimH=$singlePaired.sParams.sTrimH - --trimL=$singlePaired.sParams.sTrimL - --mismatchSeed=$singlePaired.sParams.sMismatchSeed - --mismatchQual=$singlePaired.sParams.sMismatchQual - --seedLen=$singlePaired.sParams.sSeedLen - --rounding=$singlePaired.sParams.sRounding - --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign - --tryHard=$singlePaired.sParams.sTryHard - --valAlign=$singlePaired.sParams.sValAlign - --allValAligns=$singlePaired.sParams.sAllValAligns - --suppressAlign=$singlePaired.sParams.sSuppressAlign - --best=$singlePaired.sParams.sBestOption.sBest - #if $singlePaired.sParams.sBestOption.sBest == "doBest": - --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks - --strata=$singlePaired.sParams.sBestOption.sdStrata - #else: - --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks - --strata="None" + --input1=$singlePaired.sInput1 + --params=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --skip=$singlePaired.sParams.sSkip + --alignLimit=$singlePaired.sParams.sAlignLimit + --trimH=$singlePaired.sParams.sTrimH + --trimL=$singlePaired.sParams.sTrimL + --mismatchSeed=$singlePaired.sParams.sMismatchSeed + --mismatchQual=$singlePaired.sParams.sMismatchQual + --seedLen=$singlePaired.sParams.sSeedLen + --rounding=$singlePaired.sParams.sRounding + --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign + --tryHard=$singlePaired.sParams.sTryHard + --valAlign=$singlePaired.sParams.sValAlign + --allValAligns=$singlePaired.sParams.sAllValAligns + --suppressAlign=$singlePaired.sParams.sSuppressAlign + --best=$singlePaired.sParams.sBestOption.sBest + #if $singlePaired.sParams.sBestOption.sBest == "doBest": + --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks + --strata=$singlePaired.sParams.sBestOption.sdStrata + #else: + --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks + #end if + --offrate=$singlePaired.sParams.sOffrate + --seed=$singlePaired.sParams.sSeed #end if - --offrate=$singlePaired.sParams.sOffrate - --seed=$singlePaired.sParams.sSeed - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" #else: - --input1=$singlePaired.pInput1 - --input2=$singlePaired.pInput2 - --maxInsert=$singlePaired.pMaxInsert - --mateOrient=$singlePaired.pMateOrient - --params=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --skip=$singlePaired.pParams.pSkip - --alignLimit=$singlePaired.pParams.pAlignLimit - --trimH=$singlePaired.pParams.pTrimH - --trimL=$singlePaired.pParams.pTrimL - --mismatchSeed=$singlePaired.pParams.pMismatchSeed - --mismatchQual=$singlePaired.pParams.pMismatchQual - --seedLen=$singlePaired.pParams.pSeedLen - --rounding=$singlePaired.pParams.pRounding - --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign - --minInsert=$singlePaired.pParams.pMinInsert - --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt - --forwardAlign=$singlePaired.pParams.pForwardAlign - --reverseAlign=$singlePaired.pParams.pReverseAlign - --tryHard=$singlePaired.pParams.pTryHard - --valAlign=$singlePaired.pParams.pValAlign - --allValAligns=$singlePaired.pParams.pAllValAligns - --suppressAlign=$singlePaired.pParams.pSuppressAlign - --best=$singlePaired.pParams.pBestOption.pBest - #if $singlePaired.pParams.pBestOption.pBest == "doBest": - --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks - --strata=$singlePaired.pParams.pBestOption.pdStrata - #else: - --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks - --strata="None" + --input1=$singlePaired.pInput1 + --input2=$singlePaired.pInput2 + --maxInsert=$singlePaired.pMaxInsert + --mateOrient=$singlePaired.pMateOrient + --params=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --skip=$singlePaired.pParams.pSkip + --alignLimit=$singlePaired.pParams.pAlignLimit + --trimH=$singlePaired.pParams.pTrimH + --trimL=$singlePaired.pParams.pTrimL + --mismatchSeed=$singlePaired.pParams.pMismatchSeed + --mismatchQual=$singlePaired.pParams.pMismatchQual + --seedLen=$singlePaired.pParams.pSeedLen + --rounding=$singlePaired.pParams.pRounding + --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign + --minInsert=$singlePaired.pParams.pMinInsert + --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt + --forwardAlign=$singlePaired.pParams.pForwardAlign + --reverseAlign=$singlePaired.pParams.pReverseAlign + --tryHard=$singlePaired.pParams.pTryHard + --valAlign=$singlePaired.pParams.pValAlign + --allValAligns=$singlePaired.pParams.pAllValAligns + --suppressAlign=$singlePaired.pParams.pSuppressAlign + --best=$singlePaired.pParams.pBestOption.pBest + #if $singlePaired.pParams.pBestOption.pBest == "doBest": + --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks + --strata=$singlePaired.pParams.pBestOption.pdStrata + #else: + --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks + #end if + --offrate=$singlePaired.pParams.pOffrate + --seed=$singlePaired.pParams.pSeed #end if - --offrate=$singlePaired.pParams.pOffrate - --seed=$singlePaired.pParams.pSeed - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --minInsert="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - #end if #end if </command><inputs> @@ -199,12 +113,6 @@ <when value="indexed"><param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"><options from_data_table="bowtie_indexes"/> - </param></when><when value="history"> @@ -418,7 +326,8 @@ chrM_base needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /> @@ -475,7 +384,8 @@ chrM_base is the index files' location/base name. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /><param name="sSettingsType" value="full" /> --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -1,31 +1,28 @@ -<tool id="megablast_wrapper" name="Megablast" version="1.0.5"> +<tool id="megablast_wrapper" name="Megablast" version="1.1.0"><description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> - megablast_wrapper.py - --db_build="$source_select" - --input=$input_query - --word_size=$word_size - --identity_cutoff=$iden_cutoff - --eval_cutoff=$evalue_cutoff - --filter_query=$filter_query - --index_dir=${GALAXY_DATA_INDEX_DIR} - --output=$output1 + megablast_wrapper.py + --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --input=$input_query + --word_size=$word_size + --identity_cutoff=$iden_cutoff + --eval_cutoff=$evalue_cutoff + --filter_query=$filter_query + --index_dir=${GALAXY_DATA_INDEX_DIR} + --output=$output1 </command><inputs><param name="input_query" type="data" format="fasta" label="Compare these sequences"/><param name="source_select" type="select" display="radio" label="against target database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="0"/> - </options> + <options from_data_table="blastdb" /></param> - <param name="word_size" type="select" label="using word size" help="Size of best perfect match"> + <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)"><option value="28">28</option><option value="16">16</option></param> - <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> - <param name="filter_query" type="select" label="Filter out low complexity regions?"> + <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" /> + <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)"><option value="T">Yes</option><option value="F">No</option></param> @@ -40,7 +37,7 @@ <test><param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> - <param name="source_select" value="phiX" /> + <param name="source_select" value="/galaxy/data/blastdb/phiX/phiX" /><param name="word_size" value="28" /><param name="iden_cutoff" value="99.0" /><param name="evalue_cutoff" value="10.0" /> --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -1,31 +1,37 @@ #This is a sample file distributed with Galaxy that enables tools -#to use a directory of colorspace Bowtie indexed sequences data files. -#You will need to create these data files and then create a -#bowtie_indices_color.loc file similar to this one (store it in this -#directory) that points to the directories in which those files are -#stored. The bowtie_indices_color.loc file has this format (white -#space characters are TAB characters): +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): # -#<build><file_base> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, -#then the bowtie_indices_color.loc entry would look like this: +#then the bowtie_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: # #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 gh18.3.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt #...etc... # -#Your bowtie_indices_color.loc file should include an entry per line -#for each index set you have stored. The "file" in the path does not -#actually exist, but it is the prefix for the actual index files. For -#example: +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: # -#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 -#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -1,30 +1,44 @@ -<tool id="bwa_wrapper" name="Map with BWA" version="1.0.3"> +<tool id="bwa_wrapper" name="Map with BWA" version="1.1.0"><description></description> - <command interpreter="python">bwa_wrapper.py ---threads="4" -#if $genomeSource.refGenomeSource == "history": ---ref=$genomeSource.ownFile -#else: ---ref=$genomeSource.indices -#end if ---fastq=$paired.input1 -#if $paired.sPaired == "paired": ---rfastq=$paired.input2 -#else: ---rfastq="None" -#end if ---output=$output --genAlignType=$paired.sPaired --params=$params.source_select --fileSource=$genomeSource.refGenomeSource -#if $params.source_select == "pre_set": ---maxEditDist="None" --fracMissingAligns="None" --maxGapOpens="None" --maxGapExtens="None" --disallowLongDel="None" --disallowIndel="None" --seed="None" --maxEditDistSeed="None" --mismatchPenalty="None" --gapOpenPenalty="None" --gapExtensPenalty="None" --suboptAlign="None" --noIterSearch="None" --outputTopN="None" --maxInsertSize="None" --maxOccurPairing="None" -#else: ---maxEditDist=$params.maxEditDist --fracMissingAligns=$params.fracMissingAligns --maxGapOpens=$params.maxGapOpens --maxGapExtens=$params.maxGapExtens --disallowLongDel=$params.disallowLongDel --disallowIndel=$params.disallowIndel --seed=$params.seed --maxEditDistSeed=$params.maxEditDistSeed --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty --suboptAlign=$params.suboptAlign --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing -#end if -#if $genomeSource.refGenomeSource == "history": ---dbkey=$dbkey -#else: ---dbkey="None" -#end if ---suppressHeader=$suppressHeader + <command interpreter="python"> + bwa_wrapper.py + --threads="4" + #if $genomeSource.refGenomeSource == "history": + ##build index on the fly + --ref="${genomeSource.ownFile}" + --dbkey=$dbkey + #else: + ##use precomputed indexes + --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --do_not_build_index=True + #end if + --fastq=$paired.input1 + #if $paired.sPaired == "paired": + --rfastq=$paired.input2 + #end if + --output=$output + --genAlignType=$paired.sPaired + --params=$params.source_select + --fileSource=$genomeSource.refGenomeSource + #if $params.source_select != "pre_set": + --maxEditDist=$params.maxEditDist + --fracMissingAligns=$params.fracMissingAligns + --maxGapOpens=$params.maxGapOpens + --maxGapExtens=$params.maxGapExtens + --disallowLongDel=$params.disallowLongDel + --disallowIndel=$params.disallowIndel + --seed=$params.seed + --maxEditDistSeed=$params.maxEditDistSeed + --mismatchPenalty=$params.mismatchPenalty + --gapOpenPenalty=$params.gapOpenPenalty + --gapExtensPenalty=$params.gapExtensPenalty + --suboptAlign=$params.suboptAlign + --noIterSearch=$params.noIterSearch + --outputTopN=$params.outputTopN + --maxInsertSize=$params.maxInsertSize + --maxOccurPairing=$params.maxOccurPairing + #end if + --suppressHeader=$suppressHeader </command><requirements><requirement type='package'>bwa</requirement> @@ -38,12 +52,6 @@ <when value="indexed"><param name="indices" type="select" label="Select a reference genome"><options from_data_table="bwa_indexes"/> - </param></when><when value="history"> @@ -62,7 +70,7 @@ <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/><param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/></when> - </conditional> + </conditional><conditional name="params"><param name="source_select" type="select" label="BWA settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List"><option value="pre_set">Commonly Used</option> @@ -110,12 +118,13 @@ <param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> +  + <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /><param name="source_select" value="pre_set" /> @@ -155,18 +164,19 @@ <param name="maxOccurPairing" value="100000" /><param name="suppressHeader" value="true" /><output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" /> - </test> + </test><test><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="phiX" /> +  + <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastq" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastq" ftype="fastqsanger" /> --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.0.0"> +<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.0"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><command interpreter="python"> @@ -9,191 +9,105 @@ --suppressHeader=$suppressHeader --genomeSource=$refGenomeSource.genomeSource #if $refGenomeSource.genomeSource == "history": - #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): - --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" - --do_not_build_index - #else: - --ref=$refGenomeSource.ownFile - --indexSettings=$refGenomeSource.indexParams.indexSettings - #if $refGenomeSource.indexParams.indexSettings == "indexFull": - --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB - #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": - --ipacked=$refGenomeSource.indexParams.autoBehavior.packed - --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax - --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn - --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + ##index already exists + #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): + ##user previously built + --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" + --do_not_build_index #else: - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" + ##build index on the fly + --ref=$refGenomeSource.ownFile + --indexSettings=$refGenomeSource.indexParams.indexSettings + #if $refGenomeSource.indexParams.indexSettings == "indexFull": + --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB + #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": + --ipacked=$refGenomeSource.indexParams.autoBehavior.packed + --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax + --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn + --idcv=$refGenomeSource.indexParams.autoBehavior.dcv + #end if + --inodc=$refGenomeSource.indexParams.nodc + --inoref=$refGenomeSource.indexParams.noref + --ioffrate=$refGenomeSource.indexParams.offrate + --iftab=$refGenomeSource.indexParams.ftab + --intoa=$refGenomeSource.indexParams.ntoa + --iendian=$refGenomeSource.indexParams.endian + --iseed=$refGenomeSource.indexParams.seed + --icutoff=$refGenomeSource.indexParams.cutoff + #end if #end if - --inodc=$refGenomeSource.indexParams.nodc - --inoref=$refGenomeSource.indexParams.noref - --ioffrate=$refGenomeSource.indexParams.offrate - --iftab=$refGenomeSource.indexParams.ftab - --intoa=$refGenomeSource.indexParams.ntoa - --iendian=$refGenomeSource.indexParams.endian - --iseed=$refGenomeSource.indexParams.seed - --icutoff=$refGenomeSource.indexParams.cutoff - #else: - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" - #end if - #end if - #else: - --ref=$refGenomeSource.index - --indexSettings="None" - --iautoB="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" + #else + ##use pre-built index + --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": - --input1=$singlePaired.sInput1 - --input2="None" - --params=$singlePaired.sParams.sSettingsType - #if $singlePaired.sParams.sSettingsType == "full": - --skip=$singlePaired.sParams.sSkip - --alignLimit=$singlePaired.sParams.sAlignLimit - --trimH=$singlePaired.sParams.sTrimH - --trimL=$singlePaired.sParams.sTrimL - --mismatchSeed=$singlePaired.sParams.sMismatchSeed - --mismatchQual=$singlePaired.sParams.sMismatchQual - --seedLen=$singlePaired.sParams.sSeedLen - --rounding=$singlePaired.sParams.sRounding - --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign - --tryHard=$singlePaired.sParams.sTryHard - --valAlign=$singlePaired.sParams.sValAlign - --allValAligns=$singlePaired.sParams.sAllValAligns - --suppressAlign=$singlePaired.sParams.sSuppressAlign - --best=$singlePaired.sParams.sBestOption.sBest - #if $singlePaired.sParams.sBestOption.sBest == "doBest": - --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks - --strata=$singlePaired.sParams.sBestOption.sdStrata - #else: - --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks - --strata="None" + --input1=$singlePaired.sInput1 + --params=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --skip=$singlePaired.sParams.sSkip + --alignLimit=$singlePaired.sParams.sAlignLimit + --trimH=$singlePaired.sParams.sTrimH + --trimL=$singlePaired.sParams.sTrimL + --mismatchSeed=$singlePaired.sParams.sMismatchSeed + --mismatchQual=$singlePaired.sParams.sMismatchQual + --seedLen=$singlePaired.sParams.sSeedLen + --rounding=$singlePaired.sParams.sRounding + --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign + --tryHard=$singlePaired.sParams.sTryHard + --valAlign=$singlePaired.sParams.sValAlign + --allValAligns=$singlePaired.sParams.sAllValAligns + --suppressAlign=$singlePaired.sParams.sSuppressAlign + --best=$singlePaired.sParams.sBestOption.sBest + #if $singlePaired.sParams.sBestOption.sBest == "doBest": + --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks + --strata=$singlePaired.sParams.sBestOption.sdStrata + #else: + --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks + #end if + --offrate=$singlePaired.sParams.sOffrate + --seed=$singlePaired.sParams.sSeed + --snpphred=$singlePaired.sParams.sSnpphred + --snpfrac=$singlePaired.sParams.sSnpfrac + --keepends=$singlePaired.sParams.sKeepends #end if - --offrate=$singlePaired.sParams.sOffrate - --seed=$singlePaired.sParams.sSeed - --snpphred=$singlePaired.sParams.sSnpphred - --snpfrac=$singlePaired.sParams.sSnpfrac - --keepends=$singlePaired.sParams.sKeepends - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" #else: - --input1=$singlePaired.pInput1 - --input2=$singlePaired.pInput2 - --maxInsert=$singlePaired.pMaxInsert - --mateOrient=$singlePaired.pMateOrient - --params=$singlePaired.pParams.pSettingsType - #if $singlePaired.pParams.pSettingsType == "full": - --skip=$singlePaired.pParams.pSkip - --alignLimit=$singlePaired.pParams.pAlignLimit - --trimH=$singlePaired.pParams.pTrimH - --trimL=$singlePaired.pParams.pTrimL - --mismatchSeed=$singlePaired.pParams.pMismatchSeed - --mismatchQual=$singlePaired.pParams.pMismatchQual - --seedLen=$singlePaired.pParams.pSeedLen - --rounding=$singlePaired.pParams.pRounding - --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign - --minInsert=$singlePaired.pParams.pMinInsert - --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt - --forwardAlign=$singlePaired.pParams.pForwardAlign - --reverseAlign=$singlePaired.pParams.pReverseAlign - --tryHard=$singlePaired.pParams.pTryHard - --valAlign=$singlePaired.pParams.pValAlign - --allValAligns=$singlePaired.pParams.pAllValAligns - --suppressAlign=$singlePaired.pParams.pSuppressAlign - --best=$singlePaired.pParams.pBestOption.pBest - #if $singlePaired.pParams.pBestOption.pBest == "doBest": - --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks - --strata=$singlePaired.pParams.pBestOption.pdStrata - #else: - --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks - --strata="None" + --input1=$singlePaired.pInput1 + --input2=$singlePaired.pInput2 + --maxInsert=$singlePaired.pMaxInsert + --mateOrient=$singlePaired.pMateOrient + --params=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --skip=$singlePaired.pParams.pSkip + --alignLimit=$singlePaired.pParams.pAlignLimit + --trimH=$singlePaired.pParams.pTrimH + --trimL=$singlePaired.pParams.pTrimL + --mismatchSeed=$singlePaired.pParams.pMismatchSeed + --mismatchQual=$singlePaired.pParams.pMismatchQual + --seedLen=$singlePaired.pParams.pSeedLen + --rounding=$singlePaired.pParams.pRounding + --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign + --minInsert=$singlePaired.pParams.pMinInsert + --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt + --forwardAlign=$singlePaired.pParams.pForwardAlign + --reverseAlign=$singlePaired.pParams.pReverseAlign + --tryHard=$singlePaired.pParams.pTryHard + --valAlign=$singlePaired.pParams.pValAlign + --allValAligns=$singlePaired.pParams.pAllValAligns + --suppressAlign=$singlePaired.pParams.pSuppressAlign + --best=$singlePaired.pParams.pBestOption.pBest + #if $singlePaired.pParams.pBestOption.pBest == "doBest": + --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks + --strata=$singlePaired.pParams.pBestOption.pdStrata + #else: + --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks + #end if + --offrate=$singlePaired.pParams.pOffrate + --seed=$singlePaired.pParams.pSeed + --snpphred=$singlePaired.pParams.pSnpphred + --snpfrac=$singlePaired.pParams.pSnpfrac + --keepends=$singlePaired.pParams.pKeepends #end if - --offrate=$singlePaired.pParams.pOffrate - --seed=$singlePaired.pParams.pSeed - --snpphred=$singlePaired.pParams.pSnpphred - --snpfrac=$singlePaired.pParams.pSnpfrac - --keepends=$singlePaired.pParams.pKeepends - #else: - --skip="None" - --alignLimit="None" - --trimH="None" - --trimL="None" - --mismatchSeed="None" - --mismatchQual="None" - --seedLen="None" - --rounding="None" - --maqSoapAlign="None" - --minInsert="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - --tryHard="None" - --valAlign="None" - --allValAligns="None" - --suppressAlign="None" - --best="None" - --maxBacktracks="None" - --strata="None" - --offrate="None" - --seed="None" - --snpphred="None" - --snpfrac="None" - --keepends="None" - #end if #end if </command><inputs> @@ -204,10 +118,7 @@ </param><when value="indexed"><param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="bowtie_indices_color.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="bowtie_indexes_color"/></param></when><when value="history"> @@ -433,7 +344,8 @@ chrM_color needs to be the base location/name of the index files. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/cs/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /><param name="sSettingsType" value="preSet" /> @@ -492,7 +404,8 @@ chrM_base is the index files' location/base name. --><param name="genomeSource" value="indexed" /> - <param name="index" value="equCab2chrM" /> +  + <param name="index" value="/galaxy/data/equCab2_chrM/bowtie_index/cs/chrM" /><param name="sPaired" value="single" /><param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /><param name="sSettingsType" value="full" /> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.5"><description>Search protein database with protein query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -37,9 +37,10 @@ blastp </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -1,7 +1,8 @@ #This is a sample file distributed with Galaxy that is used to define a -#list of nucelotide BLAST databases, using two columns tab separated: +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): # -#<database caption><path to base name> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -11,7 +12,7 @@ #is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry #would look like this: # -#nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk # #and your /depot/data2/galaxy/blastdb/nt directory would contain all of #your "base names" (e.g.): @@ -24,9 +25,14 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# --- a/test-data/bwa_wrapper_out2.sam +++ b/test-data/bwa_wrapper_out2.sam @@ -1,30 +1,30 @@ -seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 -seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 -seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII -seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 -seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 -seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 -seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 -seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 -seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII -seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 --- a/test-data/lastz_wrapper_out3.tabular +++ b/test-data/lastz_wrapper_out3.tabular @@ -1,26 +1,22 @@ -phiX 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG -phiX 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC -phiX 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA -phiX 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT -phiX 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT -phiX 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT -phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:646:59 18 19 - 36 C T CATTTCCATGCGGTGCACTTTATGCGGACACTTCC CATTTCCATGCGGTGCATTTTATGCGGACACTTCC -phiX 1649 1650 + 5386 HWI-EAS91_1_306UPAAXX:6:1:295:694 24 25 + 36 A G GTGATTACTTCATGCAGCGTTACCATGATGTTATTT GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT -phiX 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT -phiX 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC -phiX 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC -phiX 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC -phiX 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG -phiX 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT -phiX 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC -phiX 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA -phiX 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC -phiX 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT -phiX 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG -phiX 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG -phiX 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC -phiX 4783 4784 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1566:499 9 10 + 36 C T TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG -phiX 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG -phiX 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC -phiX 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA -phiX 4517 4518 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1485:741 19 20 - 36 G A GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT +phiX174 1164 1165 + 5386 HWI-EAS91_1_306UPAAXX:6:1:112:1280 26 27 + 36 G T GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG +phiX174 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC +phiX174 2205 2206 + 5386 HWI-EAS91_1_306UPAAXX:6:1:217:737 14 15 + 36 G T GTTCAGTTGTTGCAGTGGAATA GTTCAGTTGTTGCATTGGAATA +phiX174 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT +phiX174 578 579 + 5386 HWI-EAS91_1_306UPAAXX:6:1:317:1411 8 9 + 36 G T GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT +phiX174 2992 2993 + 5386 HWI-EAS91_1_306UPAAXX:6:1:458:1629 23 24 + 36 G T GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT +phiX174 1995 1996 + 5386 HWI-EAS91_1_306UPAAXX:6:1:590:331 14 15 + 36 G T GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT +phiX174 3261 3262 + 5386 HWI-EAS91_1_306UPAAXX:6:1:221:1238 17 18 - 36 C A AAGTCTGCCGCTGATAAAGGAAAGGATAC AAGTCTGCCGATGATAAAGGAAAGGATAC +phiX174 4109 4110 + 5386 HWI-EAS91_1_306UPAAXX:6:1:478:252 12 13 - 36 C A ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC +phiX174 3126 3127 + 5386 HWI-EAS91_1_306UPAAXX:6:1:589:96 28 29 - 36 A G CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC +phiX174 2569 2570 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1472:716 23 24 + 36 G T TGGTAATGGTGGTTTTCTTCATTGCATTCAG TGGTAATGGTGGTTTTCTTCATTTCATTCAG +phiX174 2972 2973 + 5386 HWI-EAS91_1_306UPAAXX:6:1:836:1204 17 18 + 36 G T TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT +phiX174 2234 2235 + 5386 HWI-EAS91_1_306UPAAXX:6:1:172:1412 13 14 - 36 C A AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC +phiX174 2902 2903 + 5386 HWI-EAS91_1_306UPAAXX:6:1:540:1415 18 19 + 36 G T TTATTAAAGAGATTATTTGTCTCCAGCCACTTA TTATTAAAGAGATTATTTTTCTCCAGCCACTTA +phiX174 2837 2838 + 5386 HWI-EAS91_1_306UPAAXX:6:1:253:1162 14 15 - 36 T A ATGGTTTGGTCTAACTTTACCGCTACTAAATGC ATGGTTTGGTCAAACTTTACCGCTACTAAATGC +phiX174 4662 4663 + 5386 HWI-EAS91_1_306UPAAXX:6:1:828:754 26 27 + 36 G T TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT +phiX174 4202 4203 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 19 20 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 4206 4207 + 5386 HWI-EAS91_1_306UPAAXX:6:1:891:1437 23 24 + 36 G T TAATGGTGATATGTATGTTGACGGCCATAAGGCTG TAATGGTGATATGTATGTTTACGTCCATAAGGCTG +phiX174 430 431 + 5386 HWI-EAS91_1_306UPAAXX:6:1:203:667 9 10 - 36 T C AGACCGCTTTGGCCTCTATTAAGC AGACCGCCTTGGCCTCTATTAAGC +phiX174 2857 2858 + 5386 HWI-EAS91_1_306UPAAXX:6:1:578:971 15 16 + 36 G T CGCTACTAAATGCCGCGGATTGGTTTCG CGCTACTAAATTCCGCGGATTGGTTTCG +phiX174 3112 3113 + 5386 HWI-EAS91_1_306UPAAXX:6:1:1721:1800 27 28 - 36 T C TCAAGGCTCTAATGTTCCTAACCC TCAAGGCTCTAATGTCCCTAACCC +phiX174 4825 4826 + 5386 HWI-EAS91_1_306UPAAXX:6:1:815:1640 9 10 - 36 T G CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -29,15 +29,12 @@ def stop_err( msg ): def __main__(): #Parse Command Line options, args = doc_optparse.parse( __doc__ ) - - db_build = options.db_build query_filename = options.input.strip() output_filename = options.output.strip() mega_word_size = options.word_size # -W mega_iden_cutoff = options.identity_cutoff # -p mega_evalue_cutoff = options.eval_cutoff # -e mega_temp_output = tempfile.NamedTemporaryFile().name - mega_filter = options.filter_query # -F GALAXY_DATA_INDEX_DIR = options.index_dir DB_LOC = "%s/blastdb.loc" % GALAXY_DATA_INDEX_DIR @@ -47,30 +44,20 @@ def __main__(): except: stop_err( 'Invalid value for word size' ) try: - float(mega_iden_cutoff) + float( mega_iden_cutoff ) except: stop_err( 'Invalid value for identity cut-off' ) try: - float(mega_evalue_cutoff) + float( mega_evalue_cutoff ) except: stop_err( 'Invalid value for Expectation value' ) - # prepare the database - db = {} - for i, line in enumerate( file( DB_LOC ) ): - line = line.rstrip( '\r\n' ) - if not line or line.startswith( '#' ): - continue - fields = line.split( '\t' ) - db[ fields[0] ] = fields[1] + if not os.path.exists( os.path.split( options.db_build )[0] ): + stop_err( 'Cannot locate the target database directory. Please check your location file.' ) - if not db.has_key( db_build ): - stop_err( 'Cannot locate the target database. Please check your location file.' ) - - # arguments for megablast - chunk = db[ ( db_build ) ] - megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null " \ - % ( chunk, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, mega_filter ) + # arguments for megablast + megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null" \ + % ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) print megablast_command --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -3,15 +3,15 @@ #to create these data files and then create a srma_index.loc file #similar to this one (store it in this directory) that points to #the directories in which those files are stored. The srma_index.loc -#file has this format (white space is the TAB character): +#file has this format (longer white space is the TAB character): # -#<build><fasta_file> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 /depot/data2/galaxy/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: @@ -23,3 +23,4 @@ #created via Picard (http://picard.sourceforge.net) Note that #the dict file does not have the .fa extension although the #path list in the loc file does include it. +# --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -1,20 +1,21 @@ -<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> +<tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.1.0"><description> map short paired reads against reference sequence</description><command interpreter="python">lastz_paired_reads_wrapper.py -#if $seq_name.how_to_name=="yes": ---ref_name=$seq_name.ref_name -#else: ---ref_name="None" -#end if ---ref_source=$source.ref_source --input2=$input2 --input3=$input3 --input4=$input4 -#if $source.ref_source=="history": ---input1=$source.input1 ---ref_sequences=$input1.metadata.sequences -#else: ---input1=$source.input1_2bit ---ref_sequences="None" -#end if ---output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} + #if $seq_name.how_to_name=="yes": + --ref_name=$seq_name.ref_name + #end if + --ref_source=$source.ref_source + --input2=$input2 + --input3=$input3 + --input4=$input4 + #if $source.ref_source=="history": + --input1=$source.input1 + --ref_sequences=$input1.metadata.sequences + #else: + --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + #end if + --output=$output1 + --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} </command><inputs><param name="input2" format="fasta" type="data" label="Align sequencing reads in" /> @@ -25,10 +26,7 @@ </param><when value="cached"><param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="lastz_seqs.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> + <options from_data_table="lastz_seqs" /></param></when><when value="history"> @@ -64,7 +62,7 @@ --><param name="input2" value="lastz_paired_input2.fasta" ftype="fasta" /><param name="ref_source" value="cached" /> - <param name="input1_2bit" value="hg18Chr21" /> + <param name="input1_2bit" value="/galaxy/data/hg18/seq/chr21.2bit" /><param name="input3" value="lastz_paired_input3.fasta" ftype="fasta" /><param name="input4" value="lastz_paired_input4.qual454" ftype="qual454" /><param name="how_to_name" value="no" /> --- a/tools/sr_mapping/lastz_wrapper.py +++ b/tools/sr_mapping/lastz_wrapper.py @@ -156,7 +156,7 @@ def __main__(): unmask = '[unmask]' else: unmask = '' - if options.ref_name != 'None': + if options.ref_name: ref_name = '[nickname=%s]' % options.ref_name else: ref_name = '' --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.5"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -35,9 +35,10 @@ tblastx </param><when value="db"><param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.5"><description>Search protein database with translated nucleotide query sequence(s)</description><command> ## The command is a Cheetah template which allows some Python based syntax. @@ -36,9 +36,10 @@ blastx </param><when value="db"><param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> + <column name="name" index="2"/> + <column name="value" index="0"/></options></param><param name="subject" type="hidden" value="" /> --- a/test-data/perm_in1.fastqsanger +++ b/test-data/perm_in1.fastqsanger @@ -1,76 +1,76 @@ @HWI-EAS91_1_30788AAXX:1:1:1761:343/1 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA -+/1 ++ IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII @HWI-EAS91_1_30788AAXX:1:1:1578:331/1 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1647:512/1 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1570:620/1 GAGTAACAAAGTaaaGTTTGGAccGTTTTTGTCTCGTGCTCGTCGCTGCG -+/1 ++ IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1599:330/1 AGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1652:270/1 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGacTTTGCATTGTTTAATTG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1746:351/1 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1582:633/1 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1598:534/1 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1572:324/1 AAGGTGCTTaaaTTCgtGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1749:466/1 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1629:446/1 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1763:587/1 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1616:363/1 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1768:715/1 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1572:270/1 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT -+/1 ++ III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1673:514/1 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII @HWI-EAS91_1_30788AAXX:1:1:1634:330/1 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG -+/1 ++ IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -1,17 +1,37 @@ <tables> +  + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table><table name="bfast_indexes" comment_char="#"><columns>value, dbkey, formats, name, path</columns><file path="tool-data/bfast_indexes.loc" /></table> +  + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> + </table> +  + <table name="blastdb_p" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb_p.loc" /> + </table> - <table name="bowtie_indexes"> - <columns>name, value</columns> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns><file path="tool-data/bowtie_indices.loc" /></table> +  + <table name="bowtie_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices_color.loc" /> + </table> - <table name="bwa_indexes"> - <columns>name, value</columns> + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns><file path="tool-data/bwa_index.loc" /></table> @@ -24,4 +44,30 @@ <columns>value, dbkey, name, path</columns><file path="tool-data/ngs_sim_fasta.loc" /></table> +  + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +  + <table name="perm_base_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_base_index.loc" /> + </table> +  + <table name="perm_color_indexes" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/perm_color_index.loc" /> + </table> +  + <table name="srma_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/srma_index.loc" /> + </table> +  +</tables> --- a/test-data/phiX.fasta +++ b/test-data/phiX.fasta @@ -1,109 +1,79 @@ ->phiX -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTG -ATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTA -CGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTA -TCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACT -AACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATA -TGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT -CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGT -TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA -TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG -ACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTG -CGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCT -TTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT -CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGT -TCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGAC -GCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATG -TCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTT -GCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG -GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATT -ATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTA -CTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC -CGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACAT -TTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA -AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT -ACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATAC -CAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAAT -GAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAA -AAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAA -TGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT -GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCg -TGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC -GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACA -GACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA -TGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT -CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGA -CCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG -TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAG -TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCG -TACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT -GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT -TGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTT -CAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTA -AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT -AATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC -TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTA -AATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACC -CTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGG -TTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT -ACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT -TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGG -CGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAG -GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC -GATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCA -AGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCT -GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGG -CAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTG -CATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT -GCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAAT -GCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA -AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTAC -TGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGC -AGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGT -CAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGC -TGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT -CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCT -GCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTA -ATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTT -TTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCC -TTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA -AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATG -CTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGAT -TCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTT -ACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCA -ACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT -GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCT -GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAA -GAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGA -AATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGA -CGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT -TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAAT -GATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTAC -AGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTC -CTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGC -CAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC -CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTT -GGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGC -TGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGC -TGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTC -GGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCA -ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCC -GACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG -CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +

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galaxy-dist commit c61ec9e333d5: Enable gff2bed tool to convert GFF3 files to BED and add functional test for this conversion.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1289243703 18000 # Node ID c61ec9e333d5a0ade7a23b3f4b55ae3deb3aa0bb # Parent 629e14c5f561446c963b05560f245e2ed7041ff0 Enable gff2bed tool to convert GFF3 files to BED and add functional test for this conversion. --- a/tools/filters/gff2bed.xml +++ b/tools/filters/gff2bed.xml @@ -16,6 +16,11 @@ <param name="input" value="gff2bed_in2.gff" ftype="gff"/><output name="out_file1" file="gff2bed_out2.bed"/></test> + <test> +  + <param name="input" value="5.gff3" ftype="gff"/> + <output name="out_file1" file="gff2bed_out3.bed"/> + </test></tests><help> --- /dev/null +++ b/test-data/gff2bed_out3.bed @@ -0,0 +1,145 @@ +ctgA 22131 24633 my_feature 0 + +ctgA 46989 48410 my_feature 0 - +ctgA 44704 47713 my_feature 0 - +ctgA 36648 40440 my_feature 0 - +ctgA 23071 23185 my_feature 0 + +ctgA 37241 38653 my_feature 0 + +ctgA 37496 40559 motif 0 - +ctgA 36033 38167 my_feature 0 + +ctgA 28331 30033 motif 0 - +ctgA 4714 5968 my_feature 0 - +ctgA 48252 48366 motif 0 + +ctgA 999 20000 BAC 0 + +ctgA 19499 20000 right_end_read 0 - +ctgA 999 1500 left_end_read 0 + +ctgA 13800 14007 motif 0 - +ctgA 1049 9000 coding 0 + +ctgA 1200 1500 CDS 0 + +ctgA 2999 3902 CDS 0 + +ctgA 4999 5500 CDS 0 + +ctgA 6999 7608 CDS 0 + +ctgA 1049 9000 processed_transcript 0 + +ctgA 1049 1200 5'-UTR 0 + +ctgA 7608 9000 3'-UTR 0 + +ctgA 5409 7503 match 0 - +ctgA 6999 7503 HSP 0 - +ctgA 5409 5500 HSP 0 - +ctgA 46011 48851 motif 0 + +ctgA 6884 8999 match 0 - +ctgA 8305 8999 HSP 0 - +ctgA 8054 8080 HSP 0 - +ctgA 7409 7737 HSP 0 - +ctgA 6884 7241 HSP 0 - +ctgA 13279 16394 my_feature 0 + +ctgA 29770 32937 match 0 + +ctgA 29770 29942 HSP 0 + +ctgA 30041 30340 HSP 0 + +ctgA 30809 31307 HSP 0 + +ctgA 31760 31984 HSP 0 + +ctgA 32373 32937 HSP 0 + +ctgA 36615 37227 match 0 - +ctgA 37207 37227 HSP 0 - +ctgA 36615 37057 HSP 0 - +ctgA 11910 15561 motif 0 + +ctgA 1049 3202 match 0 + +ctgA 1049 1500 HSP 0 + +ctgA 2999 3202 HSP 0 + +ctgA 15395 16159 motif 0 + +ctgA 1149 7200 match 0 + +ctgA 1149 1500 HSP 0 + +ctgA 4999 5500 HSP 0 + +ctgA 6999 7200 HSP 0 + +ctgA 1049 7300 match 0 + +ctgA 1049 1500 HSP 0 + +ctgA 4999 5500 HSP 0 + +ctgA 6999 7300 HSP 0 + +ctgA 19156 22915 my_feature 0 - +ctgA 7999 9000 match 0 - +ctgA 7999 9000 HSP 0 - +ctgA 28341 28447 motif 0 - +ctgA 17666 17690 motif 0 + +ctgA 44400 45925 trace 0 + +ctgA 26121 34466 match 0 + +ctgA 26121 26126 HSP 0 + +ctgA 26496 26869 HSP 0 + +ctgA 27200 27325 HSP 0 + +ctgA 27371 27433 HSP 0 + +ctgA 27564 27565 HSP 0 + +ctgA 27812 28091 HSP 0 + +ctgA 28092 28201 HSP 0 + +ctgA 28328 28377 HSP 0 + +ctgA 28828 29194 HSP 0 + +ctgA 29516 29702 HSP 0 + +ctgA 29712 30061 HSP 0 + +ctgA 30328 30774 HSP 0 + +ctgA 30807 31306 HSP 0 + +ctgA 31515 31729 HSP 0 + +ctgA 31752 32154 HSP 0 + +ctgA 32594 32696 HSP 0 + +ctgA 32891 32901 HSP 0 + +ctgA 33126 33388 HSP 0 + +ctgA 33438 33443 HSP 0 + +ctgA 33758 34209 HSP 0 + +ctgA 34400 34466 HSP 0 + +ctgA 0 50000 contig 0 + +ctgA 41136 47829 match 0 - +ctgA 47448 47829 HSP 0 - +ctgA 46815 46992 HSP 0 - +ctgA 46091 46318 HSP 0 - +ctgA 45789 46022 HSP 0 - +ctgA 45230 45488 HSP 0 - +ctgA 44762 45030 HSP 0 - +ctgA 44064 44556 HSP 0 - +ctgA 43394 43811 HSP 0 - +ctgA 42889 43270 HSP 0 - +ctgA 42056 42474 HSP 0 - +ctgA 41753 41948 HSP 0 - +ctgA 41136 41318 HSP 0 - +ctgA 12530 15870 match 0 + +ctgA 12530 12895 HSP 0 + +ctgA 13121 13449 HSP 0 + +ctgA 13451 13745 HSP 0 + +ctgA 13907 13965 HSP 0 + +ctgA 13997 14488 HSP 0 + +ctgA 14563 14899 HSP 0 + +ctgA 15184 15276 HSP 0 + +ctgA 15638 15736 HSP 0 + +ctgA 15744 15870 HSP 0 + +ctgA 7499 8000 match 0 - +ctgA 7499 8000 HSP 0 - +ctgA 1299 9000 coding 0 + +ctgA 3300 3902 CDS 0 + +ctgA 4999 5500 CDS 0 + +ctgA 6999 7600 CDS 0 + +ctgA 1299 9000 processed_transcript 0 + +ctgA 1299 1500 5'-UTR 0 + +ctgA 2999 3300 5'-UTR 0 + +ctgA 7600 9000 3'-UTR 0 + +ctgA 26502 35904 match 0 - +ctgA 35641 35904 HSP 0 - +ctgA 35332 35507 HSP 0 - +ctgA 34604 34983 HSP 0 - +ctgA 34243 34313 HSP 0 - +ctgA 33437 33868 HSP 0 - +ctgA 33052 33325 HSP 0 - +ctgA 32207 32680 HSP 0 - +ctgA 32009 32057 HSP 0 - +ctgA 31420 31817 HSP 0 - +ctgA 31231 31236 HSP 0 - +ctgA 30464 30798 HSP 0 - +ctgA 30107 30216 HSP 0 - +ctgA 29512 29647 HSP 0 - +ctgA 28776 29058 HSP 0 - +ctgA 28224 28316 HSP 0 - +ctgA 27886 28076 HSP 0 - +ctgA 27447 27860 HSP 0 - +ctgA 27171 27185 HSP 0 - +ctgA 26502 26799 HSP 0 - +ctgA 49405 50000 match 0 + +ctgA 49405 49476 HSP 0 + +ctgA 49761 50000 HSP 0 + +ctgA 1049 9000 gene 0 + +ctgA 33324 35791 motif 0 + +ctgA 31784 32359 match 0 + +ctgA 31784 31939 HSP 0 + +ctgA 32328 32359 HSP 0 + --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -42,13 +42,18 @@ def convert_gff_coords_to_bed( interval def parse_gff_attributes( attr_str ): """ - Parses a GFF attribute string and returns a dictionary of name-value pairs. - The general format for a GFF attribute string is name1 "value1" ; name2 "value2" + Parses a GFF/GTF attribute string and returns a dictionary of name-value pairs. + The general format for a GFF3 attributes string is name1=value1;name2=value2 + The general format for a GTF attribute string is name1 "value1" ; name2 "value2" """ attributes_list = attr_str.split(";") attributes = {} for name_value_pair in attributes_list: + # Try splitting by space and, if necessary, by '=' sign. pair = name_value_pair.strip().split(" ") + if len( pair ) == 1: + pair = name_value_pair.strip().split("=") + print pair if pair == '': continue name = pair[0].strip()

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galaxy-dist commit d344c55b4f81: another tiny rgHaploView tool test fix - pdfs differ on Main by 20kb.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Ross Lazarus <ross.lazarus(a)gmail.com> # Date 1289244501 18000 # Node ID d344c55b4f81f273d712c397d648fbaf308a9beb # Parent 629e14c5f561446c963b05560f245e2ed7041ff0 another tiny rgHaploView tool test fix - pdfs differ on Main by 20kb. --- a/tools/rgenetics/rgHaploView.xml +++ b/tools/rgenetics/rgHaploView.xml @@ -1,5 +1,4 @@ -<tool id="rgHaploView1" name="LD plots:"> - <code file="rgHaploView_code.py"/> +<tool id="rgHaploView1" name="LD plots:" version="0.2"><description>and comparisons with HapMap data</description> @@ -16,7 +15,7 @@ label="Current history lPed format data" size="80" help="Linkage Ped format data from your current history" /> - <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL)" + <param name="ucsc_region" type="text" label="Optional subset region (blank=ALL. WARNING: doing this will fail if >1 chromosome in input data!)" size="80" optional="true" help="Region eg: chr9:119,506,000-119,518,000 Leave blank for all or to extract the rs list supplied below."/> @@ -53,7 +52,7 @@ <param name="infoTrack" type="select" label="Add Hapmap information track to image" help="Refseq genes and snp density can be added to the plot if desired for orientation" > - <option value="info">Add Information track (DISABLED! Awaiting fix from Haploview authors)</option> + <option value="info">Add Information track (DISABLED! Awaiting bug fix from Haploview authors since reported in October 2009)</option><option value="noinfo" selected="True">No Information track</option></param> @@ -75,8 +74,7 @@ </inputs><outputs> - <data format="html" name="out_file1" /> - + <data format="html" name="out_file1" label="${title}.html" /></outputs><!-- python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \ @@ -101,9 +99,9 @@ <param name='infoTrack' value='noinfo' /><param name='hires' value='lo' /><param name='memsize' value='2048' /> - <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="50"> - <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="3000"/> - <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="3000" /> + <output name='out_file1' file='rgtestouts/rgHaploView/rgHaploViewtest1.html' ftype='html' lines_diff="60"> + <extra_files type="file" name='alljoin.pdf' value="rgtestouts/rgHaploView/alljoin.pdf" compare="sim_size" delta="50000"/> + <extra_files type="file" name='allnup.pdf' value="rgtestouts/rgHaploView/allnup.pdf" compare="sim_size" delta="50000" /><extra_files type="file" name='Log_rgHaploViewtest1.txt' value="rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt" compare="diff" lines_diff="50"/><extra_files type="file" name='rgHaploViewtest1.ped.TESTS' value="rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS" compare="diff" lines_diff="20"/>

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