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January 2010

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[hg] galaxy 3225: Added SOLiD (colorspace) support to Bowtie wra...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/56efe838b9af changeset: 3225:56efe838b9af user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Jan 11 17:04:45 2010 -0500 description: Added SOLiD (colorspace) support to Bowtie wrapper tool diffstat: test-data/bowtie_in1.fastqsanger | 4 + test-data/bowtie_in2.fastqsanger | 5 + test-data/bowtie_in3.fastqsanger | 4 + test-data/bowtie_in4.fastqsanger | 4 + test-data/bowtie_in5.fastqsanger | 4 + test-data/bowtie_in6.fastqsanger | 4 + test-data/bowtie_out1.sam | 2 +- test-data/bowtie_out2.sam | 3 +- test-data/bowtie_out3.sam | 4 +- test-data/bowtie_out4.sam | 2 + test-data/bowtie_out5.sam | 1 + test-data/bowtie_out6.sam | 1 + test-data/bowtie_out7.sam | 2 + test-data/bowtie_out8.sam | 2 + tool-data/bowtie_indices_color.loc.sample | 31 + tools/sr_mapping/bowtie_wrapper.py | 447 ++++++-- tools/sr_mapping/bowtie_wrapper.xml | 1391 +++++++++++++++++++++------- tools/sr_mapping/bowtie_wrapper_code.py | 18 +- 18 files changed, 1402 insertions(+), 527 deletions(-) diffs (2080 lines): diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in1.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G21022233110003122233210021301222000112122113330022 ++ +=;8:?@=?;;9:8;=>;5A?;<8><<=:9><;9<=8;96>8<5==:<98; \ No newline at end of file diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in2.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,5 @@ +@HWI-EAS91_1_30788AAXX:1:1:1513:715/1 +GTTTTTTNNGCATAGATGTTTAGTTGTGGTAGTCAG ++/1 +IIIIIII""IIIIIIIIIIIIIIIIIIIDI?II-+I + diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in3.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/1 +G2102223311000312223321002 ++ +=;8:?@=?;;9:8;=>;5A?;<8>< diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in4.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in4.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,4 @@ +@869_1532_1255/2 +2200333112212110002221031T ++ +;89<:==5<8>69;8=<9;<>9:=< diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in5.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in5.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,4 @@ +@HWI-EAS91_1_30788AAXX:1:2:618:346/1 +TAGACTACGAAAGTGACTTTAATACCTCTGACTACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_in6.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_in6.fastqsanger Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,4 @@ +@HWI-EAS91_1_30788AAXX:1:2:618:346/2 +ATAGGCTGAATTAGCAATGGATGGTGGGGTTTATCG ++ +IIIIIIIIIIIIIII9I.II5II6DFIIIIII*I2) diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out1.sam --- a/test-data/bowtie_out1.sam Mon Jan 11 16:35:16 2010 -0500 +++ b/test-data/bowtie_out1.sam Mon Jan 11 17:04:45 2010 -0500 @@ -1,1 +1,1 @@ -HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 +869_1532_1255/1 16 chrM 3728 255 48M * 0 0 GAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAGAGG "TUVYQPSUSNSRTXTSVYVRVXWYUSVY_UOXZWRQRSUY[\^XQR! XA:i:1 MD:Z:48 NM:i:0 CM:i:2 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out2.sam --- a/test-data/bowtie_out2.sam Mon Jan 11 16:35:16 2010 -0500 +++ b/test-data/bowtie_out2.sam Mon Jan 11 17:04:45 2010 -0500 @@ -1,2 +1,1 @@ -HWI-EAS91_1_30788AAXX:1:2:618:346/1 99 chrM 441 255 36M = 652 247 TAGACTACGAAAGTGACTTTAATACCTCTGACTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3 XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:2:618:346/2 147 chrM 652 255 36M = 441 -247 CGATAAACCCCACCATCCATTGCTAATTCAGCCTAT )2I*IIIIIIFD6II5II.I9IIIIIIIIIIIIIII XA:i:1 MD:Z:18C17 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out3.sam --- a/test-data/bowtie_out3.sam Mon Jan 11 16:35:16 2010 -0500 +++ b/test-data/bowtie_out3.sam Mon Jan 11 17:04:45 2010 -0500 @@ -1,2 +1,2 @@ -HWI-EAS91_1_30788AAXX:1:2:618:346/1 99 chrM 441 255 36M = 652 247 TAGACTACGAAAGTGACTTTAATACCTCTGACTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3 XA:i:0 MD:Z:36 NM:i:0 -HWI-EAS91_1_30788AAXX:1:2:618:346/2 147 chrM 652 255 36M = 441 -247 CGATAAACCCCACCATCCATTGCTAATTCAGCCTAT )2I*IIIIIIFD6II5II.I9IIIIIIIIIIIIIII XA:i:0 MD:Z:18C17 NM:i:1 +869_1532_1255 163 chrM 3727 255 27M = 3752 50 GGAAATATGTCTGACAAAAGAGTTACT !!PTUVYQPSUSNSRTXTSVYVRVX<! XA:i:2 MD:Z:27 NM:i:0 CM:i:2 +869_1532_1255 83 chrM 3752 255 25M = 3727 -50 CTTTGATAGAGTAAAACATAGAGGC >USVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:25 NM:i:0 CM:i:1 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out4.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out4.sam Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,2 @@ +HWI-EAS91_1_30788AAXX:1:2:618:346 99 chrM 441 255 36M = 652 247 TAGACTACGAAAGTGACTTTAATACCTCTGACTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3 XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:2:618:346 147 chrM 652 255 36M = 441 -247 CGATAAACCCCACCATCCATTGCTAATTCAGCCTAT )2I*IIIIIIFD6II5II.I9IIIIIIIIIIIIIII XA:i:1 MD:Z:18C17 NM:i:1 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out5.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out5.sam Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,1 @@ +869_1532_1255/1 16 chrM 3727 255 50M * 0 0 GGAAATATGTCTGACAAAAGAGTTACTTTGATAGAGTAAAACATAGAGGC !"TUVYQPSUSNSRTXTSVYVRVXWYUSVY_UOXZWRQRSUY[\^XQR!! XA:i:1 MD:Z:50 NM:i:0 CM:i:2 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out6.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out6.sam Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,1 @@ +HWI-EAS91_1_30788AAXX:1:1:1513:715/1 16 chrM 9563 255 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII XA:i:2 MD:Z:27A0G7 NM:i:2 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out7.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out7.sam Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,2 @@ +869_1532_1255 163 chrM 3728 255 25M = 3752 47 GAAATATGTCTGACAAAAGAGTTAC !PTUVYQPSUSNSRTXTSVYVRVX< XA:i:2 MD:Z:25 NM:i:0 CM:i:2 +869_1532_1255 83 chrM 3753 255 23M = 3727 -49 TTTGATAGAGTAAAACATAGAGG USVY_UOXZWRQRSUY[\^XQR! XA:i:1 MD:Z:23 NM:i:0 CM:i:1 diff -r 61f1ec6c5b24 -r 56efe838b9af test-data/bowtie_out8.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie_out8.sam Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,2 @@ +HWI-EAS91_1_30788AAXX:1:2:618:346 99 chrM 441 255 36M = 652 247 TAGACTACGAAAGTGACTTTAATACCTCTGACTACA IIIIIIIIIIIIIIIIIIIIIIIIIIIII%4II;I3 XA:i:0 MD:Z:36 NM:i:0 +HWI-EAS91_1_30788AAXX:1:2:618:346 147 chrM 652 255 36M = 441 -247 CGATAAACCCCACCATCCATTGCTAATTCAGCCTAT )2I*IIIIIIFD6II5II.I9IIIIIIIIIIIIIII XA:i:1 MD:Z:18C17 NM:i:1 diff -r 61f1ec6c5b24 -r 56efe838b9af tool-data/bowtie_indices_color.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices_color.loc.sample Mon Jan 11 17:04:45 2010 -0500 @@ -0,0 +1,31 @@ +#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): +# +#<build> <file_base> +# +#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: +# +#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 +#...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: +# +#hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 diff -r 61f1ec6c5b24 -r 56efe838b9af tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Jan 11 16:35:16 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Jan 11 17:04:45 2010 -0500 @@ -2,6 +2,61 @@ """ Runs Bowtie on single-end or paired-end data. +For use with Bowtie v. 0.12.1 + +usage: bowtie_wrapper.py [options] + -t, --threads=t: The number of threads to run + -i, --input1=i: The (forward or single-end) reads file in Sanger FASTQ format + -I, --input2=I: The reverse reads file in Sanger FASTQ format + -o, --output=o: The output file + -4, --dataType=4: The type of data (SOLiD or Solexa) + -2, --paired=2: Whether the data is single- or paired-end + -g, --genomeSource=g: The type of reference provided + -r, --ref=r: The reference genome to use or index + -s, --skip=s: Skip the first n reads + -a, --alignLimit=a: Only align the first n reads + -T, --trimH=T: Trim n bases from high-quality (left) end of each read before alignment + -L, --trimL=L: Trim n bases from low-quality (right) end of each read before alignment + -m, --mismatchSeed=m: Maximum number of mismatches permitted in the seed + -M, --mismatchQual=M: Maximum permitted total of quality values at mismatched read positions + -l, --seedLen=l: Seed length + -n, --rounding=n: Whether or not to round to the nearest 10 and saturating at 30 + -P, --maqSoapAlign=P: Choose MAQ- or SOAP-like alignment policy + -w, --tryHard=: Whether or not to try as hard as possible to find valid alignments when they exist + -v, --valAlign=v: Report up to n valid arguments per read + -V, --allValAligns=V: Whether or not to report all valid alignments per read + -G, --suppressAlign=G: Suppress all alignments for a read if more than n reportable alignments exist + -b, --best=b: Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions + -B, --maxBacktracks=B: Maximum number of backtracks permitted when aligning a read + -R, --strata=R: Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable + -j, --minInsert=j: Minimum insert size for valid paired-end alignments + -J, --maxInsert=J: Maximum insert size for valid paired-end alignments + -O, --mateOrient=O: The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand + -A, --maxAlignAttempt=A: Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate + -f, --forwardAlign=f: Whether or not to attempt to align the forward reference strand + -E, --reverseAlign=E: Whether or not to attempt to align the reverse-complement reference strand + -F, --offrate=F: Override the offrate of the index to n + -8, --snpphred=8: SNP penalty on Phred scale + -6, --snpfrac=6: Fraction of sites expected to be SNP sites + -7, --keepends=7: Keep extreme-end nucleotides and qualities + -S, --seed=S: Seed for pseudo-random number generator + -d, --dbkey=d: Dbkey of reference genome + -C, --params=C: Whether to use default or specified parameters + -u, --iauto_b=u: Automatic or specified behavior + -K, --ipacked=K: Whether or not to use a packed representation for DNA strings + -Q, --ibmax=Q: Maximum number of suffixes allowed in a block + -Y, --ibmaxdivn=Y: Maximum number of suffixes allowed in a block as a fraction of the length of the reference + -D, --idcv=D: The period for the difference-cover sample + -U, --inodc=U: Whether or not to disable the use of the difference-cover sample + -y, --inoref=y: Whether or not to build the part of the reference index used only in paired-end alignment + -z, --ioffrate=z: How many rows get marked during annotation of some or all of the Burrows-Wheeler rows + -W, --iftab=W: The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query + -X, --intoa=X: Whether or not to convert Ns in the reference sequence to As + -N, --iendian=N: Endianness to use when serializing integers to the index file + -Z, --iseed=Z: Seed for the pseudorandom number generator + -c, --icutoff=c: Number of first bases of the reference sequence to index + -x, --indexSettings=x: Whether or not indexing options are to be set + -H, --suppressHeader=H: Suppress header """ import optparse, os, shutil, sys, tempfile @@ -13,161 +68,281 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() - parser.add_option('', '--threads', dest='threads', help='The number of threads to run') - parser.add_option('', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format') - parser.add_option('', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format') - parser.add_option('', '--output', dest='output', help='The output file') - parser.add_option('', '--paired', dest='paired', help='Whether the data is single- or paired-end') - parser.add_option('', '--genomeSource', dest='genomeSource', help='The type of reference provided') - parser.add_option('', '--ref', dest='ref', help='The reference genome to use or index') - parser.add_option('', '--skip', dest='skip', help='Skip the first n reads') - parser.add_option('', '--alignLimit', dest='alignLimit', help='Only align the first n reads') - parser.add_option('', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment') - parser.add_option('', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment') - parser.add_option('', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed') - parser.add_option('', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions') - parser.add_option('', '--seedLen', dest='seedLen', help='Seed length') - parser.add_option('', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30') - parser.add_option('', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy') - parser.add_option('', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist') - parser.add_option('', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read') - parser.add_option('', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read') - parser.add_option('', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist') - parser.add_option('', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions") - parser.add_option('', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read') - parser.add_option('', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable') - parser.add_option('', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments') - parser.add_option('', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments') - parser.add_option('', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand') - parser.add_option('', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate') - parser.add_option('', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand') - parser.add_option('', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand') - parser.add_option('', '--offrate', dest='offrate', help='Override the offrate of the index to n') - parser.add_option('', '--seed', dest='seed', help='Seed for pseudo-random number generator') - parser.add_option('', '--dbkey', dest='dbkey', help='') - parser.add_option('', '--params', dest='params', help='Whether to use default or specified parameters') - parser.add_option('', '--iauto_b', dest='iauto_b', help='Automatic or specified behavior') - parser.add_option('', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings') - parser.add_option('', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block') - parser.add_option('', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference') - parser.add_option('', '--idcv', dest='idcv', help='The period for the difference-cover sample') - parser.add_option('', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample') - parser.add_option('', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paried-end alignment') - parser.add_option('', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows') - parser.add_option('', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query') - parser.add_option('', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As') - parser.add_option('', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file') - parser.add_option('', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator') - parser.add_option('', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index') - parser.add_option('', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set') - parser.add_option('', '--suppressHeader', dest='suppressHeader', help='Suppress header') + parser.add_option( '-t', '--threads', dest='threads', help='The number of threads to run' ) + parser.add_option( '-4', '--dataType', dest='dataType', help='The type of data (SOLiD or Solexa)' ) + parser.add_option( '-i', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) + parser.add_option( '-I', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '-o', '--output', dest='output', help='The output file' ) + parser.add_option( '-2', '--paired', dest='paired', help='Whether the data is single- or paired-end' ) + parser.add_option( '-g', '--genomeSource', dest='genomeSource', help='The type of reference provided' ) + parser.add_option( '-r', '--ref', dest='ref', help='The reference genome to use or index' ) + parser.add_option( '-s', '--skip', dest='skip', help='Skip the first n reads' ) + parser.add_option( '-a', '--alignLimit', dest='alignLimit', help='Only align the first n reads' ) + parser.add_option( '-T', '--trimH', dest='trimH', help='Trim n bases from high-quality (left) end of each read before alignment' ) + parser.add_option( '-L', '--trimL', dest='trimL', help='Trim n bases from low-quality (right) end of each read before alignment' ) + parser.add_option( '-m', '--mismatchSeed', dest='mismatchSeed', help='Maximum number of mismatches permitted in the seed' ) + parser.add_option( '-M', '--mismatchQual', dest='mismatchQual', help='Maximum permitted total of quality values at mismatched read positions' ) + parser.add_option( '-l', '--seedLen', dest='seedLen', help='Seed length' ) + parser.add_option( '-n', '--rounding', dest='rounding', help='Whether or not to round to the nearest 10 and saturating at 30' ) + parser.add_option( '-P', '--maqSoapAlign', dest='maqSoapAlign', help='Choose MAQ- or SOAP-like alignment policy' ) + parser.add_option( '-w', '--tryHard', dest='tryHard', help='Whether or not to try as hard as possible to find valid alignments when they exist' ) + parser.add_option( '-v', '--valAlign', dest='valAlign', help='Report up to n valid arguments per read' ) + parser.add_option( '-V', '--allValAligns', dest='allValAligns', help='Whether or not to report all valid alignments per read' ) + parser.add_option( '-G', '--suppressAlign', dest='suppressAlign', help='Suppress all alignments for a read if more than n reportable alignments exist' ) + parser.add_option( '-b', '--best', dest='best', help="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions" ) + parser.add_option( '-B', '--maxBacktracks', dest='maxBacktracks', help='Maximum number of backtracks permitted when aligning a read' ) + parser.add_option( '-R', '--strata', dest='strata', help='Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable' ) + parser.add_option( '-j', '--minInsert', dest='minInsert', help='Minimum insert size for valid paired-end alignments' ) + parser.add_option( '-J', '--maxInsert', dest='maxInsert', help='Maximum insert size for valid paired-end alignments' ) + parser.add_option( '-O', '--mateOrient', dest='mateOrient', help='The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand' ) + parser.add_option( '-A', '--maxAlignAttempt', dest='maxAlignAttempt', help='Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate' ) + parser.add_option( '-f', '--forwardAlign', dest='forwardAlign', help='Whether or not to attempt to align the forward reference strand' ) + parser.add_option( '-E', '--reverseAlign', dest='reverseAlign', help='Whether or not to attempt to align the reverse-complement reference strand' ) + parser.add_option( '-F', '--offrate', dest='offrate', help='Override the offrate of the index to n' ) + parser.add_option( '-S', '--seed', dest='seed', help='Seed for pseudo-random number generator' ) + parser.add_option( '-8', '--snpphred', dest='snpphred', help='SNP penalty on Phred scale' ) + parser.add_option( '-6', '--snpfrac', dest='snpfrac', help='Fraction of sites expected to be SNP sites' ) + parser.add_option( '-7', '--keepends', dest='keepends', help='Keep extreme-end nucleotides and qualities' ) + parser.add_option( '-d', '--dbkey', dest='dbkey', help='Dbkey of reference genome' ) + parser.add_option( '-C', '--params', dest='params', help='Whether to use default or specified parameters' ) + parser.add_option( '-u', '--iauto_b', dest='iauto_b', help='Automatic or specified behavior' ) + parser.add_option( '-K', '--ipacked', dest='ipacked', help='Whether or not to use a packed representation for DNA strings' ) + parser.add_option( '-Q', '--ibmax', dest='ibmax', help='Maximum number of suffixes allowed in a block' ) + parser.add_option( '-Y', '--ibmaxdivn', dest='ibmaxdivn', help='Maximum number of suffixes allowed in a block as a fraction of the length of the reference' ) + parser.add_option( '-D', '--idcv', dest='idcv', help='The period for the difference-cover sample' ) + parser.add_option( '-U', '--inodc', dest='inodc', help='Whether or not to disable the use of the difference-cover sample' ) + parser.add_option( '-y', '--inoref', dest='inoref', help='Whether or not to build the part of the reference index used only in paired-end alignment' ) + parser.add_option( '-z', '--ioffrate', dest='ioffrate', help='How many rows get marked during annotation of some or all of the Burrows-Wheeler rows' ) + parser.add_option( '-W', '--iftab', dest='iftab', help='The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query' ) + parser.add_option( '-X', '--intoa', dest='intoa', help='Whether or not to convert Ns in the reference sequence to As' ) + parser.add_option( '-N', '--iendian', dest='iendian', help='Endianness to use when serializing integers to the index file' ) + parser.add_option( '-Z', '--iseed', dest='iseed', help='Seed for the pseudorandom number generator' ) + parser.add_option( '-c', '--icutoff', dest='icutoff', help='Number of first bases of the reference sequence to index' ) + parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) + parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() # make temp directory for placement of indices and copy reference file there if necessary tmp_index_dir = tempfile.mkdtemp() + # get type of data (solid or solexa) + if options.dataType == 'solid': + colorspace = '-C' + else: + colorspace = '' # index if necessary - if options.genomeSource == 'history': + if options.genomeSource == 'cHistory' or options.genomeSource == 'xHistory': # set up commands - if options.index_settings =='index_pre_set': - indexing_cmds = '' + if options.index_settings =='cIndexPreSet' or options.index_settings == 'xIndexPreSet': + indexing_cmds = '%s' % colorspace else: try: - indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s' % \ - (('','--noauto')[options.iauto_b=='set'], - ('','--packed')[options.ipacked=='packed'], - ('','--bmax %s'%options.ibmax)[options.ibmax!='None' and options.ibmax>=1], - ('','--bmaxdivn %s'%options.ibmaxdivn)[options.ibmaxdivn!='None'], - ('','--dcv %s'%options.idcv)[options.idcv!='None'], - ('','--nodc')[options.inodc=='nodc'], - ('','--noref')[options.inoref=='noref'], options.ioffrate, - ('','--ftabchars %s'%options.iftab)[int(options.iftab)>=0], - ('','--ntoa')[options.intoa=='yes'], - ('--little','--big')[options.iendian=='big'], - ('','--seed %s'%options.iseed)[int(options.iseed)>0], - ('','--cutoff %s'%options.icutoff)[int(options.icutoff)>0]) + if options.iauto_b == 'set': + iauto_b = '--noauto' + else: + iauto_b = '' + if options.ipacked == 'packed': + ipacked = '--packed' + else: + ipacked = '' + if options.ibmax != 'None' and int( options.ibmax ) >= 1: + ibmax = '--bmax %s' % options.ibmax + else: + ibmax = '' + if options.ibmaxdivn != 'None' and int( options.ibmaxdivn ) >= 0: + ibmaxdivn = '--bmaxdivn %s' % options.ibmaxdivn + else: + ibmaxdivn = '' + if options.idcv != 'None' and int( options.idcv ) > 0: + idcv = '--dcv %s' % options.idcv + else: + idcv = '' + if options.inodc == 'nodc': + inodc = '--nodc' + else: + inodc = '' + if options.inoref == 'noref': + inoref = '--noref' + else: + inoref = '' + if options.iftab != 'None' and int( options.iftab ) >= 0: + iftab = '--ftabchars %s' % options.iftab + else: + iftab = '' + if options.intoa == 'yes': + intoa = '--ntoa' + else: + intoa = '' + if options.iendian == 'big': + iendian = '--big' + else: + iendian = '--little' + if int( options.iseed ) > 0: + iseed = '--seed %s' % options.iseed + else: + iseed = '' + if int( options.icutoff ) > 0: + icutoff = '--cutoff %s' % options.icutoff + else: + icutoff = '' + indexing_cmds = '%s %s %s %s %s %s %s --offrate %s %s %s %s %s %s %s' % \ + ( iauto_b, ipacked, ibmax, ibmaxdivn, idcv, inodc, + inoref, options.ioffrate, iftab, intoa, iendian, + iseed, icutoff, colorspace ) except ValueError: indexing_cmds = '' try: - shutil.copy(options.ref, tmp_index_dir) - except Exception, erf: - stop_err('Error creating temp directory for indexing purposes\n' + str(erf)) - options.ref = os.path.join(tmp_index_dir,os.path.split(options.ref)[1]) - cmd1 = 'bowtie-build %s -f %s %s 2> /dev/null' % (indexing_cmds, options.ref, options.ref) + shutil.copy( options.ref, tmp_index_dir ) + except Exception, e: + stop_err( 'Error creating temp directory for indexing purposes\n' + str( e ) ) + options.ref = os.path.join( tmp_index_dir, os.path.split( options.ref )[1] ) + cmd1 = 'bowtie-build %s -f %s %s 2> /dev/null' % ( indexing_cmds, options.ref, options.ref ) try: - os.chdir(tmp_index_dir) - os.system(cmd1) - except Exception, erf: - stop_err('Error indexing reference sequence\n' + str(erf)) + os.chdir( tmp_index_dir ) + os.system( cmd1 ) + except Exception, e: + stop_err( 'Error indexing reference sequence\n' + str( e ) ) # set up aligning and generate aligning command options # automatically set threads in both cases - if options.params == 'pre_set': - aligning_cmds = '-p %s -S' % options.threads + if options.suppressHeader == 'true': + suppressHeader = '--sam-nohead' + else: + suppressHeader = '' + if options.params == 'csPreSet' or options.params == 'cpPreSet' or \ + options.params == 'xsPreSet' or options.params == 'xpPreSet': + aligning_cmds = '-p %s -S %s -q %s ' % ( options.threads, suppressHeader, colorspace ) else: try: - aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ - '%s %s %s %s %s %s %s %s %s %s -p %s -S' % \ - (('','-s %s'%options.skip)[options.skip!='None'], - ('','-u %s'%options.alignLimit)[int(options.alignLimit)>0], - ('','-5 %s'%options.trimH)[int(options.trimH)>=0], - ('','-3 %s'%options.trimL)[int(options.trimL)>=0], - ('','-n %s'%options.mismatchSeed)[options.mismatchSeed=='0' or options.mismatchSeed=='1' or options.mismatchSeed=='2' or options.mismatchSeed=='3'], - ('','-e %s'%options.mismatchQual)[int(options.mismatchQual)>=0], - ('','-l %s'%options.seedLen)[int(options.seedLen)>=5], - ('','--nomaqround')[options.rounding=='noRound'], - ('','-v %s'%options.maqSoapAlign)[options.maqSoapAlign!='-1'], - ('','-I %s'%options.minInsert)[options.minInsert!='None'], - ('','-X %s'%options.maxInsert)[options.maxInsert!='None'], - ('','--%s'%options.mateOrient)[options.mateOrient!='None'], - ('','--pairtries %s'%options.maxAlignAttempt)[options.maxAlignAttempt!='None' and int(options.maxAlignAttempt)>=0], - ('','--nofw')[options.forwardAlign=='noForward'], - ('','--norc')[options.reverseAlign=='noReverse'], - ('','--maxbts %s'%options.maxBacktracks)[options.maxBacktracks!='None' and (options.mismatchSeed=='2' or options.mismatchSeed=='3')], - ('','-y')[options.tryHard=='doTryHard'], - ('','-k %s'%options.valAlign)[options.valAlign!='None' and int(options.valAlign)>=0], - ('','-a')[options.allValAligns=='doAllValAligns' and int(options.allValAligns)>=0], - ('','-m %s'%options.suppressAlign)[int(options.suppressAlign)>=0], - ('','--best')[options.best=='doBest'], - ('','--strata')[options.strata=='doStrata'], - ('','-o %s'%options.offrate)[int(options.offrate)>=0], - ('','--seed %s'%options.seed)[int(options.seed)>=0], - options.threads) - except ValueError, erf: - stop_err('Something is wrong with the alignment parameters and the alignment could not be run\n' + str(erf)) + if options.skip != 'None' and int( options.skip ) > 0: + skip = '-s %s' % options.skip + else: + skip = '' + if int( options.alignLimit ) >= 0: + alignLimit = '-u %s' % options.alignLimit + else: + alignLimit = '' + if int( options.trimH ) > 0: + trimH = '-5 %s' % options.trimH + else: + trimH = '' + if int( options.trimL ) > 0: + trimL = '-3 %s' % options.trimL + else: + trimL = '' + if options.mismatchSeed == '0' or options.mismatchSeed == '1' or options.mismatchSeed == '2' or options.mismatchSeed == '3': + mismatchSeed = '-n %s' % options.mismatchSeed + else: + mismatchSeed = '' + if int( options.mismatchQual ) >= 0: + mismatchQual = '-e %s' % options.mismatchQual + else: + mismatchQual = '' + if int( options.seedLen ) >= 5: + seedLen = '-l %s' % options.seedLen + else: + seedLen = '' + if options.rounding == 'noRound': + rounding = '--nomaqround' + else: + rounding = '' + if options.maqSoapAlign != '-1': + maqSoapAlign = '-v %s' % options.maqSoapAlign + else: + maqSoapAlign = '' + if options.minInsert != 'None' and int( options.minInsert ) > 0: + minInsert = '-I %s' % options.minInsert + else: + minInsert = '' + if options.maxInsert != 'None' and int( options.maxInsert ) > 0: + maxInsert = '-X %s' % options.maxInsert + else: + maxInsert = '' + if options.mateOrient != 'None': + mateOrient = '--%s' % options.mateOrient + else: + mateOrient = '' + if options.maxAlignAttempt != 'None' and int( options.maxAlignAttempt ) >= 0: + maxAlignAttempt = '--pairtries %s' % options.maxAlignAttempt + else: + maxAlignAttempt = '' + if options.forwardAlign == 'noForward': + forwardAlign = '--nofw' + else: + forwardAlign = '' + if options.reverseAlign == 'noReverse': + reverseAlign = '--norc' + else: + reverseAlign = '' + if options.maxBacktracks != 'None' and int( options.maxBacktracks ) > 0 and \ + ( options.mismatchSeed == '2' or options.mismatchSeed == '3' ): + maxBacktracks = '--maxbts %s' % options.maxBacktracks + else: + maxBacktracks = '' + if options.tryHard == 'doTryHard': + tryHard = '-y' + else: + tryHard = '' + if options.valAlign != 'None' and int( options.valAlign ) >= 0: + valAlign = '-k %s' % options.valAlign + else: + valAlign = '' + if options.allValAligns == 'doAllValAligns': + allValAligns = '-a' + else: + allValAligns = '' + if options.suppressAlign != 'None' and int( options.suppressAlign ) >= 0: + suppressAlign = '-m %s' % options.suppressAlign + else: + suppressAlign = '' + if options.best == 'csDoBest' or options.best == 'cpDoBest' or \ + options.best == 'xsDoBest' or options.best == 'xpDoBest': + best = '--best' + else: + best = '' + if options.strata == 'doStrata': + strata = '--strata' + else: + strata = '' + if options.offrate != 'None' and int( options.offrate ) >= 0: + offrate = '-o %s' % options.offrate + else: + offrate = '' + if options.seed != 'None' and int( options.seed ) >= 0: + seed = '--seed %s' % options.seed + else: + seed = '' + if options.snpphred != 'None' and int( options.snpphred ) >= 0: + snpphred = '--snpphred %s' % options.snpphred + else: + snpphred = '' + if options.snpfrac != 'None' and float( options.snpfrac ) >= 0: + snpfrac = '--snpfrac %s' % options.snpfrac + else: + snpfrac = '' + if options.keepends != 'None' and options.keepends == 'doKeepends': + keepends = '--col-keepends' + else: + keepends = '' + aligning_cmds = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s ' \ + '%s %s %s %s %s %s %s %s %s %s %s -p %s -S %s -q' % \ + ( skip, alignLimit, trimH, trimL, mismatchSeed, mismatchQual, + seedLen, rounding, maqSoapAlign, minInsert, maxInsert, + mateOrient, maxAlignAttempt, forwardAlign, reverseAlign, + maxBacktracks, tryHard, valAlign, allValAligns, suppressAlign, + best, strata, offrate, seed, colorspace, snpphred, snpfrac, + keepends, options.threads, suppressHeader ) + except ValueError, e: + stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) # prepare actual aligning commands - if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.input2, options.output) + if options.paired == 'cPaired' or options.paired == 'xPaired': + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.input2, options.output ) else: - cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % (aligning_cmds, options.ref, options.input1, options.output) + cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.output ) # align try: - os.system(cmd2) - except Exception, erf: - stop_err("Error aligning sequence\n" + str(erf)) - # remove header if necessary - if options.suppressHeader == 'true': - tmp_out = tempfile.NamedTemporaryFile() - cmd3 = 'cp %s %s' % (options.output, tmp_out.name) - try: - os.system(cmd3) - except Exception, erf: - stop_err("Error copying output file before removing headers\n" + str(erf)) - output = file(tmp_out.name, 'r') - fout = file(options.output, 'w') - header = True - line = output.readline() - while line.strip() != '': - if header: - if line.startswith('@HD') or line.startswith('@SQ') or line.startswith('@RG') or line.startswith('@PG') or line.startswith('@CO'): - pass - else: - header = False - fout.write(line) - else: - fout.write(line) - line = output.readline() - fout.close() - tmp_out.close() + os.system( cmd2 ) + except Exception, e: + stop_err( 'Error aligning sequence\n' + str( e ) ) # clean up temp dir - if os.path.exists(tmp_index_dir): - shutil.rmtree(tmp_index_dir) + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) if __name__=="__main__": __main__() diff -r 61f1ec6c5b24 -r 56efe838b9af tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Mon Jan 11 16:35:16 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.xml Mon Jan 11 17:04:45 2010 -0500 @@ -1,326 +1,780 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie" version="1.0.0"> +<tool id="bowtie_wrapper" name="Map with Bowtie" version="1.0.5"> <description></description> <command interpreter="python"> - bowtie_wrapper.py - --threads="4" - --input1=$singlePaired.input1 - #if $singlePaired.sPaired == "paired": - --input2=$singlePaired.input2 - #else: - --input2="None" - #end if - --output=$output - --paired=$singlePaired.sPaired - --genomeSource=$refGenomeSource.genomeSource - #if $refGenomeSource.genomeSource == "history": - --ref=$refGenomeSource.ownFile - #else: - --ref=$refGenomeSource.indices.value - #end if - --params=$singlePaired.params.settings_type - #if $singlePaired.params.settings_type == "full": - --skip=$singlePaired.params.skip - --alignLimit=$singlePaired.params.alignLimit - --trimH=$singlePaired.params.trimH - --trimL=$singlePaired.params.trimL - --mismatchSeed=$singlePaired.params.mismatchSeed - --mismatchQual=$singlePaired.params.mismatchQual - --seedLen=$singlePaired.params.seedLen - --rounding=$singlePaired.params.rounding - --maqSoapAlign=$singlePaired.params.maqSoapAlign - --tryHard=$singlePaired.params.tryHard - --valAlign=$singlePaired.params.valAlign - --allValAligns=$singlePaired.params.allValAligns - --suppressAlign=$singlePaired.params.suppressAlign - --offrate=$singlePaired.params.offrate - --seed=$singlePaired.params.seed - --best=$singlePaired.params.bestOption.best - #if $singlePaired.params.bestOption.best == "doBest": - --maxBacktracks=$singlePaired.params.bestOption.maxBacktracks - --strata=$singlePaired.params.bestOption.strata - #else: - --maxBacktracks="None" - --strata="None" - #end if - #if $singlePaired.sPaired == "single": - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - #else: - --minInsert=$singlePaired.params.minInsert - --maxInsert=$singlePaired.params.maxInsert - --mateOrient=$singlePaired.params.mateOrient - --maxAlignAttempt=$singlePaired.params.maxAlignAttempt - --forwardAlign=$singlePaired.params.forwardAlign - --reverseAlign=$singlePaired.params.reverseAlign - #end if - #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" - --minInsert="None" - --maxInsert="None" - --mateOrient="None" - --maxAlignAttempt="None" - --forwardAlign="None" - --reverseAlign="None" - --offrate="None" - --seed="None" - #end if - #if $refGenomeSource.genomeSource == "history": - --dbkey=$dbkey - #else: - --dbkey="None" - #end if - #if $refGenomeSource.genomeSource == "history": - --indexSettings=$refGenomeSource.indexParams.index_settings - #else: - --indexSettings="None" - #end if - #if $refGenomeSource.genomeSource == "history" and $refGenomeSource.indexParams.index_settings == "index_full": - --iauto_b=$refGenomeSource.indexParams.auto_behavior.auto_b - #if $refGenomeSource.indexParams.auto_behavior.auto_b == "set": - --ipacked=$refGenomeSource.indexParams.auto_behavior.packed - --ibmax=$refGenomeSource.indexParams.auto_behavior.bmax - --ibmaxdivn=$refGenomeSource.indexParams.auto_behavior.bmaxdivn - --idcv=$refGenomeSource.indexParams.auto_behavior.dcv - #else: - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - #end if - --inodc=$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=$refGenomeSource.indexParams.cutoff - #else: - --iauto_b="None" - --ipacked="None" - --ibmax="None" - --ibmaxdivn="None" - --idcv="None" - --inodc="None" - --inoref="None" - --ioffrate="None" - --iftab="None" - --intoa="None" - --iendian="None" - --iseed="None" - --icutoff="None" - #end if - --suppressHeader=$suppressHeader + bowtie_wrapper.py --threads="4" --output=$output --suppressHeader=$suppressHeader --dataType=$solidOrSolexa.dataType +#if $solidOrSolexa.dataType == "solid": + --genomeSource=$solidOrSolexa.cRefGenomeSource.cGenomeSource + #if $solidOrSolexa.cRefGenomeSource.cGenomeSource == "cIndexed": + --ref=$solidOrSolexa.cRefGenomeSource.cIndex.value + --dbkey="None" + --indexSettings="None" + --iauto_b="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: + --ref=$solidOrSolexa.cRefGenomeSource.cOwnFile + --dbkey=$dbkey + --indexSettings=$solidOrSolexa.cRefGenomeSource.cIndexParams.cIndexSettings + #if $solidOrSolexa.cRefGenomeSource.cIndexParams.cIndexSettings == "cIndexFull": + --iauto_b=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cAutoB == "cSet" + #if $solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cAutoB == "cSet": + --ipacked=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cPacked + --ibmax=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cBmax + --ibmaxdivn=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cBmaxdivn + --idcv=$solidOrSolexa.cRefGenomeSource.cIndexParams.cAutoBehavior.cDcv + #else: + --ipacked="None" + --ibmax="None" + --ibmaxdivn="None" + --idcv="None" + #end if + --inodc=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNodc + --inoref=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNoref + --ioffrate=$solidOrSolexa.cRefGenomeSource.cIndexParams.cOffrate + --iftab=$solidOrSolexa.cRefGenomeSource.cIndexParams.cFtab + --intoa=$solidOrSolexa.cRefGenomeSource.cIndexParams.cNtoa + --iendian=$solidOrSolexa.cRefGenomeSource.cIndexParams.cEndian + --iseed=$solidOrSolexa.cRefGenomeSource.cIndexParams.cSeed + --icutoff=$solidOrSolexa.cRefGenomeSource.cIndexParams.cCutoff + #else: + --iauto_b="None" + --ipacked="None" + --ibmax="None" + --ibmaxdivn="None" + --idcv="None" + --inodc="None" + --inoref="None" + --ioffrate="None" + --iftab="None" + --intoa="None" + --iendian="None" + --iseed="None" + --icutoff="None" + #end if + #end if + --paired=$solidOrSolexa.cSinglePaired.cSPaired + #if $solidOrSolexa.cSinglePaired.cSPaired == "cSingle": + --input1=$solidOrSolexa.cSinglePaired.csInput1 + --input2="None" + --params=$solidOrSolexa.cSinglePaired.csParams.csSettingsType + #if $solidOrSolexa.cSinglePaired.csParams.csSettingsType == "csFull": + --skip=$solidOrSolexa.cSinglePaired.csParams.csSkip + --alignLimit=$solidOrSolexa.cSinglePaired.csParams.csAlignLimit + --trimH=$solidOrSolexa.cSinglePaired.csParams.csTrimH + --trimL=$solidOrSolexa.cSinglePaired.csParams.csTrimL + --mismatchSeed=$solidOrSolexa.cSinglePaired.csParams.csMismatchSeed + --mismatchQual=$solidOrSolexa.cSinglePaired.csParams.csMismatchQual + --seedLen=$solidOrSolexa.cSinglePaired.csParams.csSeedLen + --rounding=$solidOrSolexa.cSinglePaired.csParams.csRounding + --maqSoapAlign=$solidOrSolexa.cSinglePaired.csParams.csMaqSoapAlign + --tryHard=$solidOrSolexa.cSinglePaired.csParams.csTryHard + --valAlign=$solidOrSolexa.cSinglePaired.csParams.csValAlign + --allValAligns=$solidOrSolexa.cSinglePaired.csParams.csAllValAligns + --suppressAlign=$solidOrSolexa.cSinglePaired.csParams.csSuppressAlign + --best=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csBest + #if $solidOrSolexa.cSinglePaired.csParams.csBestOption.csBest == "csDoBest": + --maxBacktracks=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csdMaxBacktracks + --strata=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csdStrata + #else: + --maxBacktracks=$solidOrSolexa.cSinglePaired.csParams.csBestOption.csnMaxBacktracks + --strata="None" + #end if + --offrate=$solidOrSolexa.cSinglePaired.csParams.csOffrate + --seed=$solidOrSolexa.cSinglePaired.csParams.csSeed + --snpphred=$solidOrSolexa.cSinglePaired.csParams.csSnpphred + --snpfrac=$solidOrSolexa.cSinglePaired.csParams.csSnpfrac + --keepends=$solidOrSolexa.cSinglePaired.csParams.csKeepends + #else: + --skip="None" + --alignLimit="None" + --trimH="None" + --trimL="None" + --mismatchSeed="None" + --mismatchQual="None" + --seedLen="None" + --rounding="None" + --maqSoapAlign="None" + --tryHard="None" + --valAlign="None" + --allValAligns="None" + --suppressAlign="None" + --best="None" + --maxBacktracks="None" + --strata="None" + --offrate="None" + --seed="None" + --snpphred="None" + --snpfrac="None" + --keepends="None" + #end if + --minInsert="None" + --maxInsert="None" + --mateOrient="None" + --maxAlignAttempt="None" + --forwardAlign="None" + --reverseAlign="None" + #else: + --input1=$solidOrSolexa.cSinglePaired.cpInput1 + --input2=$solidOrSolexa.cSinglePaired.cpInput2 + --params=$solidOrSolexa.cSinglePaired.cpParams.cpSettingsType + #if $solidOrSolexa.cSinglePaired.cpParams.cpSettingsType == "cpFull": + --skip=$solidOrSolexa.cSinglePaired.cpParams.cpSkip + --alignLimit=$solidOrSolexa.cSinglePaired.cpParams.cpAlignLimit + --trimH=$solidOrSolexa.cSinglePaired.cpParams.cpTrimH + --trimL=$solidOrSolexa.cSinglePaired.cpParams.cpTrimL + --mismatchSeed=$solidOrSolexa.cSinglePaired.cpParams.cpMismatchSeed + --mismatchQual=$solidOrSolexa.cSinglePaired.cpParams.cpMismatchQual + --seedLen=$solidOrSolexa.cSinglePaired.cpParams.cpSeedLen + --rounding=$solidOrSolexa.cSinglePaired.cpParams.cpRounding + --maqSoapAlign=$solidOrSolexa.cSinglePaired.cpParams.cpMaqSoapAlign + --minInsert=$solidOrSolexa.cSinglePaired.cpParams.cpMinInsert + --maxInsert=$solidOrSolexa.cSinglePaired.cpParams.cpMaxInsert + --mateOrient=$solidOrSolexa.cSinglePaired.cpParams.cpMateOrient + --maxAlignAttempt=$solidOrSolexa.cSinglePaired.cpParams.cpMaxAlignAttempt + --forwardAlign=$solidOrSolexa.cSinglePaired.cpParams.cpForwardAlign + --reverseAlign=$solidOrSolexa.cSinglePaired.cpParams.cpReverseAlign + --tryHard=$solidOrSolexa.cSinglePaired.cpParams.cpTryHard + --valAlign=$solidOrSolexa.cSinglePaired.cpParams.cpValAlign + --allValAligns=$solidOrSolexa.cSinglePaired.cpParams.cpAllValAligns + --suppressAlign=$solidOrSolexa.cSinglePaired.cpParams.cpSuppressAlign + --best=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpBest + #if $solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpBest == "cpDoBest": + --maxBacktracks=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpdMaxBacktracks + --strata=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpdStrata + #else: + --maxBacktracks=$solidOrSolexa.cSinglePaired.cpParams.cpBestOption.cpnMaxBacktracks + --strata="None" + #end if + --offrate=$solidOrSolexa.cSinglePaired.cpParams.cpOffrate + --seed=$solidOrSolexa.cSinglePaired.cpParams.cpSeed + --snpphred=$solidOrSolexa.cSinglePaired.cpParams.cpSnpphred + --snpfrac=$solidOrSolexa.cSinglePaired.cpParams.cpSnpfrac + --keepends=$solidOrSolexa.cSinglePaired.cpParams.cpKeepends + #else: + --skip="None" + --alignLimit="None" + --trimH="None" + --trimL="None" + --mismatchSeed="None" + --mismatchQual="None" + --seedLen="None" + --rounding="None" + --maqSoapAlign="None" + --tryHard="None" + --valAlign="None" + --allValAligns="None" + --suppressAlign="None" + --best="None" + --maxBacktracks="None" + --strata="None" + --offrate="None" + --seed="None" + --snpphred="None" + --snpfrac="None" + --keepends="None" + --minInsert="None" + --maxInsert="None" + --mateOrient="None" + --maxAlignAttempt="None" + --forwardAlign="None" + --reverseAlign="None" + #end if + #end if +#else: + --genomeSource=$solidOrSolexa.xRefGenomeSource.xGenomeSource + #if $solidOrSolexa.xRefGenomeSource.xGenomeSource == "xIndexed": + --ref=$solidOrSolexa.xRefGenomeSource.xIndex.value + --dbkey="None" + --indexSettings="None" + --iauto_b="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: + --ref=$solidOrSolexa.xRefGenomeSource.xOwnFile + --dbkey=$dbkey + --indexSettings=$solidOrSolexa.xRefGenomeSource.xIndexParams.xIndexSettings + #if $solidOrSolexa.xRefGenomeSource.xIndexParams.xIndexSettings == "xIndexFull": + --iauto_b=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xAutoB == "xSet" + #if $solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xAutoB == "xSet": + --ipacked=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xPacked + --ibmax=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xBmax + --ibmaxdivn=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xBmaxdivn + --idcv=$solidOrSolexa.xRefGenomeSource.xIndexParams.xAutoBehavior.xDcv + #else: + --ipacked="None" + --ibmax="None" + --ibmaxdivn="None" + --idcv="None" + #end if + --inodc=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNodc + --inoref=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNoref + --ioffrate=$solidOrSolexa.xRefGenomeSource.xIndexParams.xOffrate + --iftab=$solidOrSolexa.xRefGenomeSource.xIndexParams.xFtab + --intoa=$solidOrSolexa.xRefGenomeSource.xIndexParams.xNtoa + --iendian=$solidOrSolexa.xRefGenomeSource.xIndexParams.xEndian + --iseed=$solidOrSolexa.xRefGenomeSource.xIndexParams.xSeed + --icutoff=$solidOrSolexa.xRefGenomeSource.xIndexParams.xCutoff + #else: + --iauto_b="None" + --ipacked="None" + --ibmax="None" + --ibmaxdivn="None" + --idcv="None" + --inodc="None" + --inoref="None" + --ioffrate="None" + --iftab="None" + --intoa="None" + --iendian="None" + --iseed="None" + --icutoff="None" + #end if + #end if + --paired=$solidOrSolexa.xSinglePaired.xSPaired + #if $solidOrSolexa.xSinglePaired.xSPaired == "xSingle": + --input1=$solidOrSolexa.xSinglePaired.xsInput1 + --input2="None" + --params=$solidOrSolexa.xSinglePaired.xsParams.xsSettingsType + #if $solidOrSolexa.xSinglePaired.xsParams.xsSettingsType == "xsFull": + --skip=$solidOrSolexa.xSinglePaired.xsParams.xsSkip + --alignLimit=$solidOrSolexa.xSinglePaired.xsParams.xsAlignLimit + --trimH=$solidOrSolexa.xSinglePaired.xsParams.xsTrimH + --trimL=$solidOrSolexa.xSinglePaired.xsParams.xsTrimL + --mismatchSeed=$solidOrSolexa.xSinglePaired.xsParams.xsMismatchSeed + --mismatchQual=$solidOrSolexa.xSinglePaired.xsParams.xsMismatchQual + --seedLen=$solidOrSolexa.xSinglePaired.xsParams.xsSeedLen + --rounding=$solidOrSolexa.xSinglePaired.xsParams.xsRounding + --maqSoapAlign=$solidOrSolexa.xSinglePaired.xsParams.xsMaqSoapAlign + --tryHard=$solidOrSolexa.xSinglePaired.xsParams.xsTryHard + --valAlign=$solidOrSolexa.xSinglePaired.xsParams.xsValAlign + --allValAligns=$solidOrSolexa.xSinglePaired.xsParams.xsAllValAligns + --suppressAlign=$solidOrSolexa.xSinglePaired.xsParams.xsSuppressAlign + --best=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsBest + #if $solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsBest == "xsDoBest": + --maxBacktracks=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsdMaxBacktracks + --strata=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsdStrata + #else: + --maxBacktracks=$solidOrSolexa.xSinglePaired.xsParams.xsBestOption.xsnMaxBacktracks + --strata="None" + #end if + --offrate=$solidOrSolexa.xSinglePaired.xsParams.xsOffrate + --seed=$solidOrSolexa.xSinglePaired.xsParams.xsSeed + #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" + #end if + --snpphred="None" + --snpfrac="None" + --keepends="None" + --minInsert="None" + --maxInsert="None" + --mateOrient="None" + --maxAlignAttempt="None" + --forwardAlign="None" + --reverseAlign="None" + #else: + --input1=$solidOrSolexa.xSinglePaired.xpInput1 + --input2=$solidOrSolexa.xSinglePaired.xpInput2 + --params=$solidOrSolexa.xSinglePaired.xpParams.xpSettingsType + #if $solidOrSolexa.xSinglePaired.xpParams.xpSettingsType == "xpFull": + --skip=$solidOrSolexa.xSinglePaired.xpParams.xpSkip + --alignLimit=$solidOrSolexa.xSinglePaired.xpParams.xpAlignLimit + --trimH=$solidOrSolexa.xSinglePaired.xpParams.xpTrimH + --trimL=$solidOrSolexa.xSinglePaired.xpParams.xpTrimL + --mismatchSeed=$solidOrSolexa.xSinglePaired.xpParams.xpMismatchSeed + --mismatchQual=$solidOrSolexa.xSinglePaired.xpParams.xpMismatchQual + --seedLen=$solidOrSolexa.xSinglePaired.xpParams.xpSeedLen + --rounding=$solidOrSolexa.xSinglePaired.xpParams.xpRounding + --maqSoapAlign=$solidOrSolexa.xSinglePaired.xpParams.xpMaqSoapAlign + --minInsert=$solidOrSolexa.xSinglePaired.xpParams.xpMinInsert + --maxInsert=$solidOrSolexa.xSinglePaired.xpParams.xpMaxInsert + --mateOrient=$solidOrSolexa.xSinglePaired.xpParams.xpMateOrient + --maxAlignAttempt=$solidOrSolexa.xSinglePaired.xpParams.xpMaxAlignAttempt + --forwardAlign=$solidOrSolexa.xSinglePaired.xpParams.xpForwardAlign + --reverseAlign=$solidOrSolexa.xSinglePaired.xpParams.xpReverseAlign + --tryHard=$solidOrSolexa.xSinglePaired.xpParams.xpTryHard + --valAlign=$solidOrSolexa.xSinglePaired.xpParams.xpValAlign + --allValAligns=$solidOrSolexa.xSinglePaired.xpParams.xpAllValAligns + --suppressAlign=$solidOrSolexa.xSinglePaired.xpParams.xpSuppressAlign + --best=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpBest + #if $solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpBest == "xpDoBest": + --maxBacktracks=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpdMaxBacktracks + --strata=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpdStrata + #else: + --maxBacktracks=$solidOrSolexa.xSinglePaired.xpParams.xpBestOption.xpnMaxBacktracks + --strata="None" + #end if + --offrate=$solidOrSolexa.xSinglePaired.xpParams.xpOffrate + --seed=$solidOrSolexa.xSinglePaired.xpParams.xpSeed + #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" + --maxInsert="None" + --mateOrient="None" + --maxAlignAttempt="None" + --forwardAlign="None" + --reverseAlign="None" + #end if + --snpphred="None" + --snpfrac="None" + --keepends="None" + #end if +#end if </command> <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> + <conditional name="solidOrSolexa"> + <param name="dataType" type="select" label="Is your data SOLiD or Solexa?"> + <option value="solid">SOLiD</option> + <option value="solexa">Solexa</option> </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> - <conditional name="indexParams"> - <param name="index_settings" type="select" label="Choose whether to use default options for building indices or to set your own"> - <option value="index_pre_set">Default</option> - <option value="index_full">Set your own</option> - </param> - <when value="index_pre_set" /> - <when value="index_full"> - <conditional name="auto_behavior"> - <param name="auto_b" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> - <option value="auto">Automatic behavior</option> - <option value="set">Set values (sets --noauto and allows others to be set)</option> - </param> - <when value="auto" /> - <when value="set"> - <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (-p)"> - <option value="unpacked">Use regular representation</option> - <option value="packed">Use packed representation</option> + <when value="solid"> + <conditional name="cRefGenomeSource"> + <param name="cGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="cIndexed">Use a built-in index</option> + <option value="cHistory">Use one from the history</option> + </param> + <when value="cIndexed"> + <param name="cIndex" 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> + </param> + </when> + <when value="cHistory"> + <param name="cOwnFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + <conditional name="cIndexParams"> + <param name="cIndexSettings" type="select" label="Choose whether to use default options for building indices or to set your own"> + <option value="cIndexPreSet">Default</option> + <option value="cIndexFull">Set your own</option> + </param> + <when value="cIndexPreSet" /> + <when value="cIndexFull"> + <conditional name="cAutoBehavior"> + <param name="cAutoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> + <option value="cAuto">Automatic behavior</option> + <option value="cSet">Set values (sets --noauto and allows others to be set)</option> + </param> + <when value="cAuto" /> + <when value="cSet"> + <param name="cPacked" type="select" label="Whether or not to use a packed representation for DNA strings (-p)"> + <option value="unpacked">Use regular representation</option> + <option value="packed">Use packed representation</option> + </param> + <param name="cBmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> + <param name="cBmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> + <param name="cDcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> + </when> + </conditional> + <param name="cNodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (a very repetitive reference)"> + <option value="dc">Use difference-cover sample</option> + <option value="nodc">Disable difference-cover sample</option> </param> - <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> - <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> - <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> - </when> - </conditional> - <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (a very repetitive reference)"> - <option value="dc">Use difference-cover sample</option> - <option value="nodc">Disable difference-cover sample</option> - </param> - <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> - <option value="ref">Build all index files</option> - <option value="noref">Do not build paired-end alignment index files</option> - </param> - <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> - <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> - <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> - <option value="no">Do not convert Ns</option> - <option value="yes">Convert Ns to As</option> - </param> - <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> - <option value="little">Little</option> - <option value="big">Big</option> - </param> - <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> - <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> - </when>  - </conditional> - </when> - </conditional>  - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <conditional name="params"> - <param name="settings_type" type="select" label="Bowtie 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> - <option value="full">Full parameter list</option> - </param> - <when value="pre_set" /> - <when value="full"> - <param name="skip" type="integer" value="0" label="Skip the first n reads (-s)" /> - <param name="alignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> - <param name="trimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> - <param name="trimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> - <param name="mismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> - <param name="mismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> - <param name="seedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> - <param name="rounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> - <option value="round">Round to nearest 10</option> - <option value="noRound">Do not round to nearest 10</option> - </param> - <param name="maqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> - <param name="tryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> - <option value="noTryHard">Do not try hard</option> - <option value="doTryHard">Try hard</option> - </param> - <param name="valAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" /> - <param name="allValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> - <option value="noAllValAligns">Do not report all valid alignments</option> - <option value="doAllValAligns">Report all valid alignments</option> - </param> - <param name="suppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> - <conditional name="bestOption"> - <param name="best" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> - <option value="noBest">Do not use best</option> - <option value="doBest">Use best</option> - </param> - <when value="noBest"> - <param name="maxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - </when> - <when value="doBest"> - <param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="strata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> - <option value="noStrata">Do not use strata option</option> - <option value="doStrata">Use strata option</option> + <param name="cNoref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> + <option value="ref">Build all index files</option> + <option value="noref">Do not build paired-end alignment index files</option> </param> - </when> - </conditional>  - <param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> - </when>  - </conditional>  - </when>  - <when value="paired"> - <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"/> - <conditional name="params"> - <param name="settings_type" type="select" label="Bowtie 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> - <option value="full">Full parameter list</option> - </param> - <when value="pre_set" /> - <when value="full"> - <param name="skip" type="integer" value="0" label="Skip the first n pairs (-s)" /> - <param name="alignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> - <param name="trimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> - <param name="trimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> - <param name="mismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> - <param name="mismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> - <param name="seedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> - <param name="rounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> - <option value="round">Round to nearest 10</option> - <option value="noRound">Do not round to nearest 10</option> - </param> - <param name="maqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> - <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> - <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" /> - <param name="mateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> - <option value="fr">FR (for Illumina)</option> - <option value="rf">RF</option> - <option value="ff">FF</option> - </param> - <param name="maxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> - <param name="forwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> - <option value="forward">Align against the forward reference strand</option> - <option value="noForward">Do not align against the forward reference strand</option> - </param> - <param name="reverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> - <option value="reverse">Align against the reverse-complement reference strand</option> - <option value="noReverse">Do not align against the reverse-complement reference strand</option> - </param> - <param name="tryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> - <option value="noTryHard">Do not try hard</option> - <option value="doTryHard">Try hard</option> - </param> - <param name="valAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> - <param name="allValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> - <option value="noAllValAligns">Do not report all valid alignments</option> - <option value="doAllValAligns">Report all valid alignments</option> - </param> - <param name="suppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> - <conditional name="bestOption"> - <param name="best" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> - <option value="noBest">Do not use best</option> - <option value="doBest">Use best</option> - </param> - <when value="noBest"> - <param name="maxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - </when> - <when value="doBest"> - <param name="maxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> - <param name="strata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> - <option value="noStrata">Do not use strata option</option> - <option value="doStrata">Use strata option</option> + <param name="cOffrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> + <param name="cFtab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> + <param name="cNtoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> + <option value="no">Do not convert Ns</option> + <option value="yes">Convert Ns to As</option> </param> - </when> - </conditional> - <param name="offrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> - <param name="seed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> - </when>  - </conditional>  - </when>  - </conditional>  + <param name="cEndian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> + <option value="little">Little</option> + <option value="big">Big</option> + </param> + <param name="cSeed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> + <param name="cCutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> + </when>  + </conditional>  + </when>  + </conditional>  + <conditional name="cSinglePaired"> + <param name="cSPaired" type="select" label="Is this library mate-paired?"> + <option value="cSingle">Single-end</option> + <option value="cPaired">Paired-end</option> + </param> + <when value="cSingle"> + <param name="csInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="csParams"> + <param name="csSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="csPreSet">Commonly used</option> + <option value="csFull">Full parameter list</option> + </param> + <when value="csPreSet" /> + <when value="csFull"> + <param name="csSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> + <param name="csAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> + <param name="csTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> + <param name="csTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> + <param name="csMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> + <param name="csMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> + <param name="csSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> + <param name="csRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> + <option value="round">Round to nearest 10</option> + <option value="noRound">Do not round to nearest 10</option> + </param> + <param name="csMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> + <param name="csTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> + <option value="noTryHard">Do not try hard</option> + <option value="doTryHard">Try hard</option> + </param> + <param name="csValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" /> + <param name="csAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> + <option value="noAllValAligns">Do not report all valid alignments</option> + <option value="doAllValAligns">Report all valid alignments</option> + </param> + <param name="csSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> + <conditional name="csBestOption"> + <param name="csBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> + <option value="csNoBest">Do not use best</option> + <option value="csDoBest">Use best</option> + </param> + <when value="csNoBest"> + <param name="csnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + </when> + <when value="csDoBest"> + <param name="csdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + <param name="csdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> + <option value="noStrata">Do not use strata option</option> + <option value="doStrata">Use strata option</option> + </param> + </when> + </conditional>  + <param name="csOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> + <param name="csSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> + <param name="csSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" /> + <param name="csSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" /> + <param name="csKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--keepends)"> + <option value="doKeepends">Keep ends</option> + <option value="noKeepends">Trim ends</option> + </param> + </when>  + </conditional>  + </when>  + <when value="cPaired"> + <param name="cpInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="cpInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="cpParams"> + <param name="cpSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="cpPreSet">Commonly used</option> + <option value="cpFull">Full parameter list</option> + </param> + <when value="cpPreSet" /> + <when value="cpFull"> + <param name="cpSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> + <param name="cpAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> + <param name="cpTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> + <param name="cpTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> + <param name="cpMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> + <param name="cpMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> + <param name="cpSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> + <param name="cpRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> + <option value="round">Round to nearest 10</option> + <option value="noRound">Do not round to nearest 10</option> + </param> + <param name="cpMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> + <param name="cpMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> + <param name="cpMaxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" /> + <param name="cpMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> + <option value="fr">FR (for Illumina)</option> + <option value="rf">RF</option> + <option value="ff">FF</option> + </param> + <param name="cpMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> + <param name="cpForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> + <option value="forward">Align against the forward reference strand</option> + <option value="noForward">Do not align against the forward reference strand</option> + </param> + <param name="cpReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> + <option value="reverse">Align against the reverse-complement reference strand</option> + <option value="noReverse">Do not align against the reverse-complement reference strand</option> + </param> + <param name="cpTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> + <option value="noTryHard">Do not try hard</option> + <option value="doTryHard">Try hard</option> + </param> + <param name="cpValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> + <param name="cpAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> + <option value="noAllValAligns">Do not report all valid alignments</option> + <option value="doAllValAligns">Report all valid alignments</option> + </param> + <param name="cpSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> + <conditional name="cpBestOption"> + <param name="cpBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> + <option value="cpNoBest">Do not use best</option> + <option value="cpDoBest">Use best</option> + </param> + <when value="cpNoBest"> + <param name="cpnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + </when> + <when value="cpDoBest"> + <param name="cpdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + <param name="cpdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> + <option value="noStrata">Do not use strata option</option> + <option value="doStrata">Use strata option</option> + </param> + </when> + </conditional>  + <param name="cpOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> + <param name="cpSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> + <param name="cpSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" /> + <param name="cpSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" /> + <param name="cpKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--keepends)"> + <option value="doKeepends">Keep ends</option> + <option value="noKeepends">Trim ends</option> + </param> + </when>  + </conditional>  + </when>  + </conditional>  + </when>  + <when value="solexa"> + <conditional name="xRefGenomeSource"> + <param name="xGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> + <option value="xIndexed">Use a built-in index</option> + <option value="xHistory">Use one from the history</option> + </param> + <when value="xIndexed"> + <param name="xIndex" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> + </when> + <when value="xHistory"> + <param name="xOwnFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome" /> + <conditional name="xIndexParams"> + <param name="xIndexSettings" type="select" label="Choose whether to use default options for building indices or to set your own"> + <option value="xIndexPreSet">Default</option> + <option value="xIndexFull">Set your own</option> + </param> + <when value="xIndexPreSet" /> + <when value="xIndexFull"> + <conditional name="xAutoBehavior"> + <param name="xAutoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> + <option value="xAuto">Automatic behavior</option> + <option value="xSet">Set values (sets --noauto and allows others to be set)</option> + </param> + <when value="xAuto" /> + <when value="xSet"> + <param name="xPacked" type="select" label="Whether or not to use a packed representation for DNA strings (-p)"> + <option value="unpacked">Use regular representation</option> + <option value="packed">Use packed representation</option> + </param> + <param name="xBmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> + <param name="xBmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> + <param name="xDcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> + </when> + </conditional> + <param name="xNodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (a very repetitive reference)"> + <option value="dc">Use difference-cover sample</option> + <option value="nodc">Disable difference-cover sample</option> + </param> + <param name="xNoref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> + <option value="ref">Build all index files</option> + <option value="noref">Do not build paired-end alignment index files</option> + </param> + <param name="xOffrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> + <param name="xFtab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> + <param name="xNtoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> + <option value="no">Do not convert Ns</option> + <option value="yes">Convert Ns to As</option> + </param> + <param name="xEndian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> + <option value="little">Little</option> + <option value="big">Big</option> + </param> + <param name="xSeed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> + <param name="xCutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> + </when>  + </conditional>  + </when>  + </conditional>  + <conditional name="xSinglePaired"> + <param name="xSPaired" type="select" label="Is this library mate-paired?"> + <option value="xSingle">Single-end</option> + <option value="xPaired">Paired-end</option> + </param> + <when value="xSingle"> + <param name="xsInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="xsParams"> + <param name="xsSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="xsPreSet">Commonly used</option> + <option value="xsFull">Full parameter list</option> + </param> + <when value="xsPreSet" /> + <when value="xsFull"> + <param name="xsSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> + <param name="xsAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> + <param name="xsTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> + <param name="xsTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> + <param name="xsMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> + <param name="xsMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> + <param name="xsSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> + <param name="xsRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> + <option value="round">Round to nearest 10</option> + <option value="noRound">Do not round to nearest 10</option> + </param> + <param name="xsMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> + <param name="xsTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> + <option value="noTryHard">Do not try hard</option> + <option value="doTryHard">Try hard</option> + </param> + <param name="xsValAlign" type="integer" value="1" label="Report up to n valid arguments per read (-k)" /> + <param name="xsAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> + <option value="noAllValAligns">Do not report all valid alignments</option> + <option value="doAllValAligns">Report all valid alignments</option> + </param> + <param name="xsSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> + <conditional name="xsBestOption"> + <param name="xsBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> + <option value="xsNoBest">Do not use best</option> + <option value="xsDoBest">Use best</option> + </param> + <when value="xsNoBest"> + <param name="xsnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + </when> + <when value="xsDoBest"> + <param name="xsdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + <param name="xsdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> + <option value="noStrata">Do not use strata option</option> + <option value="doStrata">Use strata option</option> + </param> + </when> + </conditional>  + <param name="xsOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> + <param name="xsSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> + </when>  + </conditional>  + </when>  + <when value="xPaired"> + <param name="xpInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="xpInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="xpParams"> + <param name="xpSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="xpPreSet">Commonly used</option> + <option value="xpFull">Full parameter list</option> + </param> + <when value="xpPreSet" /> + <when value="xpFull"> + <param name="xpSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> + <param name="xpAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> + <param name="xpTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> + <param name="xpTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> + <param name="xpMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> + <param name="xpMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> + <param name="xpSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> + <param name="xpRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> + <option value="round">Round to nearest 10</option> + <option value="noRound">Do not round to nearest 10</option> + </param> + <param name="xpMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> + <param name="xpMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> + <param name="xpMaxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments (-X)" /> + <param name="xpMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> + <option value="fr">FR (for Illumina)</option> + <option value="rf">RF</option> + <option value="ff">FF</option> + </param> + <param name="xpMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> + <param name="xpForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> + <option value="forward">Align against the forward reference strand</option> + <option value="noForward">Do not align against the forward reference strand</option> + </param> + <param name="xpReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> + <option value="reverse">Align against the reverse-complement reference strand</option> + <option value="noReverse">Do not align against the reverse-complement reference strand</option> + </param> + <param name="xpTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> + <option value="noTryHard">Do not try hard</option> + <option value="doTryHard">Try hard</option> + </param> + <param name="xpValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> + <param name="xpAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> + <option value="noAllValAligns">Do not report all valid alignments</option> + <option value="doAllValAligns">Report all valid alignments</option> + </param> + <param name="xpSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> + <conditional name="xpBestOption"> + <param name="xpBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> + <option value="xpNoBest">Do not use best</option> + <option value="xpDoBest">Use best</option> + </param> + <when value="xpNoBest"> + <param name="xpnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + </when> + <when value="xpDoBest"> + <param name="xpdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> + <param name="xpdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> + <option value="noStrata">Do not use strata option</option> + <option value="doStrata">Use strata option</option> + </param> + </when> + </conditional>  + <param name="xpOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> + <param name="xpSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> + </when>  + </conditional>  + </when>  + </conditional>  + </when>  + </conditional>  <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information" /> </inputs> <outputs> @@ -328,83 +782,257 @@ </outputs> <tests> <test> - <param name="genomeSource" value="indexed" /> - <param name="indices" value="chrM" /> - <param name="sPaired" value="single" /> - <param name="input1" ftype="fastqsanger" value="bowtie_in1.fastq" /> - <param name="settings_type" value="pre_set" /> +  + <param name="dataType" value="solid" /> + <param name="cGenomeSource" value="cIndexed" /> + <param name="cIndex" value="equCab2chrM" /> + <param name="cSPaired" value="cSingle" /> + <param name="csInput1" ftype="fastqsanger" value="bowtie_in1.fastqsanger" /> + <param name="csSettingsType" value="csPreSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out1.sam" /> </test> <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="chr_m.fasta" /> - <param name="index_settings" value="index_pre_set" /> - <param name="sPaired" value="paired" /> - <param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" /> - <param name="input2" ftype="fastqsanger" value="bowtie_in3.fastq" /> - <param name="settings_type" value="pre_set" /> +  + <param name="dataType" value="solexa" /> + <param name="xGenomeSource" value="xIndexed" /> + <param name="xIndex" value="equCab2chrM" /> + <param name="xSPaired" value="xSingle" /> + <param name="xsInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> + <param name="xsSettingsType" value="xsPreSet" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out2.sam" /> </test> <test> - <param name="genomeSource" value="history" /> - <param name="ownFile" value="chr_m.fasta" /> - <param name="index_settings" value="index_full" /> - <param name="auto_b" value="set" /> - <param name="packed" value="unpacked" /> - <param name="bmax" value="-1" /> - <param name="bmaxdivn" value="4" /> - <param name="dcv" value="2048" /> - <param name="nodc" value="dc" /> - <param name="noref" value="noref" /> - <param name="offrate" value="6" /> - <param name="ftab" value="10" /> - <param name="ntoa" value="yes" /> - <param name="endian" value="little" /> - <param name="seed" value="-1" /> - <param name="cutoff" value="-1" /> - <param name="sPaired" value="single" /> - <param name="input1" ftype="fastqsanger" value="bowtie_in1.fastq" /> - <param name="settings_type" value="pre_set" /> - <param name="suppressHeader" value="true" /> - <output name="output" ftype="sam" file="bowtie_out1.sam" /> - </test> - <test> - <param name="genomeSource" value="indexed" /> - <param name="indices" value="chrM" /> - <param name="sPaired" value="paired" /> - <param name="input1" ftype="fastqsanger" value="bowtie_in2.fastq" /> - <param name="input2" ftype="fastqsanger" value="bowtie_in3.fastq" /> - <param name="settings_type" value="full" /> - <param name="skip" value="0" /> - <param name="alignLimit" value="-1" /> - <param name="trimL" value="0" /> - <param name="trimH" value="0" /> - <param name="mismatchSeed" value="3" /> - <param name="mismatchQual" value="50" /> - <param name="seedLen" value="10" /> - <param name="rounding" value="round" /> - <param name="maqSoapAlign" value="-1" /> - <param name="minInsert" value="0" /> - <param name="maxInsert" value="250" /> - <param name="mateOrient" value="fr" /> - <param name="maxAlignAttempt" value="100" /> - <param name="forwardAlign" value="forward" /> - <param name="reverseAlign" value="reverse" /> - <param name="tryHard" value="doTryHard" /> - <param name="valAlign" value="1" /> - <param name="allValAligns" value="noAllValAligns" /> - <param name="suppressAlign" value="-1" /> - <param name="best" value="doBest" /> - <param name="maxBacktracks" value="800" /> - <param name="strata" value="noStrata" /> - <param name="offrate" value="-1" /> - <param name="seed" value="403" /> +  + <param name="dataType" value="solid" /> + <param name="cGenomeSource" value="cHistory" /> + <param name="cOwnFile" value="chr_m.fasta" /> + <param name="cIndexSettings" value="cIndexPreSet" /> + <param name="cSPaired" value="cPaired" /> + <param name="cpInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> + <param name="cpInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="cpSettingsType" value="cpFull" /> + <param name="cpSkip" value="0" /> + <param name="cpAlignLimit" value="-1" /> + <param name="cpTrimH" value="0" /> + <param name="cpTrimL" value="0" /> + <param name="cpMismatchSeed" value="2" /> + <param name="cpMismatchQual" value="70" /> + <param name="cpSeedLen" value="28" /> + <param name="cpRounding" value="round" /> + <param name="cpMaqSoapAlign" value="-1" /> + <param name="cpMinInsert" value="0" /> + <param name="cpMaxInsert" value="250" /> + <param name="cpMateOrient" value="fr" /> + <param name="cpMaxAlignAttempt" value="100" /> + <param name="cpForwardAlign" value="forward" /> + <param name="cpReverseAlign" value="reverse" /> + <param name="cpTryHard" value="noTryHard" /> + <param name="cpValAlign" value="1" /> + <param name="cpAllValAligns" value="noAllValAligns" /> + <param name="cpSuppressAlign" value="-1" /> + <param name="cpBest" value="cpNoBest" /> + <param name="cpnMaxBacktracks" value="125" /> + <param name="cpOffrate" value="-1" /> + <param name="cpSeed" value="-1" /> + <param name="cpSnpphred" value="-1" /> + <param name="cpSnpfrac" value="0.001" /> + <param name="cpKeepends" value="doKeepends" /> <param name="suppressHeader" value="true" /> <output name="output" ftype="sam" file="bowtie_out3.sam" /> </test> + <test> +  + <param name="dataType" value="solexa" /> + <param name="xGenomeSource" value="xHistory" /> + <param name="xOwnFile" value="chr_m.fasta" /> + <param name="xIndexSettings" value="xIndexPreSet" /> + <param name="xSPaired" value="xPaired" /> + <param name="xpInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> + <param name="xpInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> + <param name="xpSettingsType" value="xpFull" /> + <param name="xpSkip" value="0" /> + <param name="xpAlignLimit" value="-1" /> + <param name="xpTrimH" value="0" /> + <param name="xpTrimL" value="0" /> + <param name="xpMismatchSeed" value="2" /> + <param name="xpMismatchQual" value="70" /> + <param name="xpSeedLen" value="28" /> + <param name="xpRounding" value="round" /> + <param name="xpMaqSoapAlign" value="-1" /> + <param name="xpMinInsert" value="0" /> + <param name="xpMaxInsert" value="250" /> + <param name="xpMateOrient" value="fr" /> + <param name="xpMaxAlignAttempt" value="100" /> + <param name="xpForwardAlign" value="forward" /> + <param name="xpReverseAlign" value="reverse" /> + <param name="xpTryHard" value="noTryHard" /> + <param name="xpValAlign" value="1" /> + <param name="xpAllValAligns" value="noAllValAligns" /> + <param name="xpSuppressAlign" value="-1" /> + <param name="xpBest" value="xpDoBest" /> + <param name="xpdMaxBacktracks" value="800" /> + <param name="xpdStrata" value="noStrata" /> + <param name="xpOffrate" value="-1" /> + <param name="xpSeed" value="-1" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out4.sam" /> + </test> +  +  + <test> +  + <param name="dataType" value="solid" /> + <param name="cGenomeSource" value="cHistory" /> + <param name="cOwnFile" value="chr_m.fasta" /> + <param name="cIndexSettings" value="cIndexFull" /> + <param name="cAutoB" value="cSet" /> + <param name="cPacked" value="unpacked" /> + <param name="cBmax" value="-1" /> + <param name="cBmaxdivn" value="4" /> + <param name="cDcv" value="1024" /> + <param name="cNodc" value="dc" /> + <param name="cNoref" value="ref" /> + <param name="cOffrate" value="5" /> + <param name="cFtab" value="10" /> + <param name="cNtoa" value="no" /> + <param name="cEndian" value="little" /> + <param name="cSeed" value="-1" /> + <param name="cCutoff" value="-1" /> + <param name="cSPaired" value="cPaired" /> + <param name="cpInput1" ftype="fastqsanger" value="bowtie_in3.fastqsanger" /> + <param name="cpInput2" ftype="fastqsanger" value="bowtie_in4.fastqsanger" /> + <param name="cpSettingsType" value="cpPreSet" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out7.sam" /> + </test> + <test> +  + <param name="dataType" value="solexa" /> + <param name="xGenomeSource" value="xHistory" /> + <param name="xOwnFile" value="chr_m.fasta" /> + <param name="xIndexSettings" value="xIndexFull" /> + <param name="xAutoB" value="xAuto" /> + <param name="xNodc" value="dc" /> + <param name="xNoref" value="ref" /> + <param name="xOffrate" value="5" /> + <param name="xFtab" value="10" /> + <param name="xNtoa" value="no" /> + <param name="xEndian" value="little" /> + <param name="xSeed" value="-1" /> + <param name="xCutoff" value="-1" /> + <param name="xSPaired" value="xPaired" /> + <param name="xpInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> + <param name="xpInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> + <param name="xpSettingsType" value="xpPreSet" /> + <param name="suppressHeader" value="true" /> + <output name="output" ftype="sam" file="bowtie_out8.sam" /> + </test> </tests> + <help> **What it does** @@ -526,6 +1154,9 @@ --strata Best strata. When running in best mode, report alignments that fall into the best stratum if there are ones falling into more than one. [off] -o <int> Offrate override. Override the offrate of the index with <int>. Some row markings are discarded when index read into memory. <int> must be greater than the value used to build the index (default: 5). [off] --seed <int> Random seed. Use <int> as the seed for the pseudo-random number generator. [off] + --snpphred <int> Use <int> as the SNP penalty for decoding colorspace alignments. True ratio of SNPs per base in the subject genome. [see --snpfrac] + --snpfrac <dec> Use <dec> as the estimated ratio of SNPs per base when decoding colorspace alignments. [0.001] + --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace alignments. [off] </help> <code file="bowtie_wrapper_code.py" /> diff -r 61f1ec6c5b24 -r 56efe838b9af tools/sr_mapping/bowtie_wrapper_code.py --- a/tools/sr_mapping/bowtie_wrapper_code.py Mon Jan 11 16:35:16 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper_code.py Mon Jan 11 17:04:45 2010 -0500 @@ -2,15 +2,21 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['refGenomeSource']['indices'].value + try: + refFile = param_dict[ 'solidOrSolexa' ][ 'cRefGenomeSource' ][ 'cIndex' ].value + except: + refFile = param_dict[ 'solidOrSolexa' ][ 'xRefGenomeSource' ][ 'xIndex' ].value except: try: - refFile = param_dict['refGenomeSource']['ownFile'].dbkey + try: + refFile = param_dict[ 'solidOrSolexa' ][ 'cRefGenomeSource' ][ 'cOwnFile' ].dbkey + except: + refFile = param_dict[ 'solidOrSolexa' ][ 'xRefGenomeSource' ][ 'xOwnFile' ].dbkey except: - out_data['output'].set_dbkey('?') + out_data[ 'output' ].set_dbkey( '?' ) return - dbkey = os.path.split(refFile)[1].split('.')[0] + dbkey = os.path.split( refFile )[1].split( '.' )[0] # deal with the one odd case - if dbkey.find('chrM') >= 0: + if dbkey.find( 'chrM' ) >= 0 or dbkey.find( 'chr_m' ) >= 0: dbkey = 'equCab2' - out_data['output'].set_dbkey(dbkey) + out_data[ 'output' ].set_dbkey(dbkey)

1 0

[hg] galaxy 3224: Enhance test framework to handle testing multi...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/61f1ec6c5b24 changeset: 3224:61f1ec6c5b24 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jan 11 16:35:16 2010 -0500 description: Enhance test framework to handle testing multiple outputs from tools. diffstat: test/functional/test_toolbox.py | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (16 lines): diff -r 658bfde702a1 -r 61f1ec6c5b24 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Mon Jan 11 13:26:00 2010 -0500 +++ b/test/functional/test_toolbox.py Mon Jan 11 16:35:16 2010 -0500 @@ -60,9 +60,9 @@ page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[i], all_inputs) self.submit_form( **page_inputs ) print "page_inputs (%i)" % i, page_inputs - # Check the result - assert len( testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet." - for name, file, sort in testdef.outputs: + # Check the results ( handles single or multiple tool outputs ) + for output_tuple in testdef.outputs: + name, file, sort = output_tuple self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds, sort=sort ) self.delete_history( id=self.security.encode_id( latest_history.id ) )

1 0

[hg] galaxy 3223: Enhance lastz tool, enhance functional test fr...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/658bfde702a1 changeset: 3223:658bfde702a1 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jan 11 13:26:00 2010 -0500 description: Enhance lastz tool, enhance functional test framework, and fix a bug in¬†editing permissions on a folder: - until now,¬†lastz will (mostly) ignore alignments in masked regions since¬†soft-masking has been enabled. ¬†Now the default has changed to disable soft masking, and an option has been added to the tool to enable it if desired. - the functional test framework now allows for a new "sort" attribute in the output tag for functional tests. ¬†For example: ¬†<output name="output1" file="lastz_wrapper_out4.tabular" sort="True" /> If set to True, the output dataset will be sorted prior to comparing. ¬†This is needed for the lastz tool since multiple threads generate output randomly if the input file has more than 1 sequence. ¬†The default is False. - Decode the id of a folder prior when retrieving from the database - fixes the bug reported by Guru. diffstat: lib/galaxy/tools/__init__.py | 3 +- lib/galaxy/tools/test.py | 4 +- lib/galaxy/web/controllers/library_common.py | 2 +- test-data/lastz_wrapper_out2.sam | 7 + test-data/lastz_wrapper_out4.tabular | 948 +++++++++++++------------- test/base/twilltestcase.py | 8 +- test/functional/test_toolbox.py | 4 +- tools/sr_mapping/lastz_wrapper.py | 14 +- tools/sr_mapping/lastz_wrapper.xml | 116 ++- 9 files changed, 579 insertions(+), 527 deletions(-) diffs (1365 lines): diff -r 60afd81f678b -r 658bfde702a1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Jan 11 12:07:58 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Mon Jan 11 13:26:00 2010 -0500 @@ -531,7 +531,8 @@ file = attrib.pop( 'file', None ) if file is None: raise Exception( "Test output does not have a 'file'") - test.add_output( name, file ) + sort = util.string_as_bool( attrib.pop( 'sort', False ) ) + test.add_output( name, file, sort ) except Exception, e: test.error = True test.exception = e diff -r 60afd81f678b -r 658bfde702a1 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Mon Jan 11 12:07:58 2010 -0500 +++ b/lib/galaxy/tools/test.py Mon Jan 11 13:26:00 2010 -0500 @@ -30,8 +30,8 @@ self.required_files.append( ( value, extra ) ) except: pass self.inputs.append( ( name, value, extra ) ) - def add_output( self, name, file ): - self.outputs.append( ( name, file ) ) + def add_output( self, name, file, sort ): + self.outputs.append( ( name, file, sort ) ) def __expand_grouping_for_data_input( self, name, value, extra, grouping_name, grouping_value ): # Currently handles grouping.Conditional and grouping.Repeat if isinstance( grouping_value, grouping.Conditional ): diff -r 60afd81f678b -r 658bfde702a1 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Jan 11 12:07:58 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Mon Jan 11 13:26:00 2010 -0500 @@ -285,7 +285,7 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( int( id ) ) + folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) if not folder: msg = "Invalid folder specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', diff -r 60afd81f678b -r 658bfde702a1 test-data/lastz_wrapper_out2.sam --- a/test-data/lastz_wrapper_out2.sam Mon Jan 11 12:07:58 2010 -0500 +++ b/test-data/lastz_wrapper_out2.sam Mon Jan 11 13:26:00 2010 -0500 @@ -59,6 +59,7 @@ 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 * @@ -175,6 +176,7 @@ 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 * @@ -192,6 +194,7 @@ 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 * @@ -360,11 +363,13 @@ 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 * @@ -421,6 +426,7 @@ 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 * @@ -433,6 +439,7 @@ 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 * diff -r 60afd81f678b -r 658bfde702a1 test-data/lastz_wrapper_out4.tabular --- a/test-data/lastz_wrapper_out4.tabular Mon Jan 11 12:07:58 2010 -0500 +++ b/test-data/lastz_wrapper_out4.tabular Mon Jan 11 13:26:00 2010 -0500 @@ -1,491 +1,491 @@ -36 phiX1 + 2310 229 228 264 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 228 NA -36 phiX1 + 2310 2071 2070 2106 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA +14 phiX1 + 2310 2192 2191 2213 22 GTTCAGTTGTTGCAGTGGAATA HWI-EAS91_1_306UPAAXX + 36 1 0 22 1 0 22 22 GTTCAGTTGTTGCATTGGAATA ..............x....... 22M 21/22 95.5% 22/36 61.1% 0/22 0.0% 2191 NA +16 phiX1 + 2310 424 423 447 24 AGACCGCTTTGGCCTCTATTAAGC HWI-EAS91_1_306UPAAXX - 36 3 2 26 11 10 34 24 AGACCGCCTTGGCCTCTATTAAGC .......:................ 24M 23/24 95.8% 24/36 66.7% 0/24 0.0% 421 NA +16 phiX2 + 3076 788 787 811 24 TCAAGGCTCTAATGTTCCTAACCC HWI-EAS91_1_306UPAAXX - 36 13 12 36 1 0 24 24 TCAAGGCTCTAATGTCCCTAACCC ...............:........ 24M 23/24 95.8% 24/36 66.7% 0/24 0.0% 775 NA +18 phiX1 + 2310 657 656 674 18 AACATTCAAACGGCCTGT HWI-EAS91_1_306UPAAXX - 36 19 18 36 1 0 18 18 AACATTCAAACGGCCTGT .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 638 NA +18 phiX2 + 3076 1421 1420 1438 18 GAATCAGCGGTATGGCTC HWI-EAS91_1_306UPAAXX + 36 1 0 18 1 0 18 18 GAATCAGCGGTATGGCTC .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 1420 NA +18 phiX2 + 3076 2625 2624 2642 18 TCTGGTTGGTTGTGGCCT HWI-EAS91_1_306UPAAXX + 36 1 0 18 1 0 18 18 TCTGGTTGGTTGTGGCCT .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 2624 NA +19 phiX2 + 3076 1874 1873 1908 35 TAATGGTGATATGTATGTTGACGGCCATAAGGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAATGGTGATATGTATGTTTACGTCCATAAGGCTG ...................x...x........... 35M 33/35 94.3% 35/36 97.2% 0/35 0.0% 1873 NA +20 phiX2 + 3076 537 536 564 28 CGCTACTAAATGCCGCGGATTGGTTTCG HWI-EAS91_1_306UPAAXX + 36 5 4 32 5 4 32 28 CGCTACTAAATTCCGCGGATTGGTTTCG ...........x................ 28M 27/28 96.4% 28/36 77.8% 0/28 0.0% 532 NA +20 phiX2 + 3076 628 627 647 20 GTGCTATTGCTGGCGGTATT HWI-EAS91_1_306UPAAXX + 36 1 0 20 1 0 20 20 GTGCTATTGCTGGCGGTATT .................... 20M 20/20 100.0% 20/36 55.6% 0/20 0.0% 627 NA +21 phiX1 + 2310 1 0 21 21 GAGTTTTATCGCTTCCATGAC HWI-EAS91_1_306UPAAXX - 36 16 15 36 1 0 21 21 GAGTTTTATCGCTTCCATGAC ..................... 21M 21/21 100.0% 21/36 58.3% 0/21 0.0% -15 -21 +21 phiX2 + 3076 1990 1989 2010 21 AACTTGATATTAATAACACTA HWI-EAS91_1_306UPAAXX - 36 16 15 36 1 0 21 21 AACTTGATATTAATAACACTA ..................... 21M 21/21 100.0% 21/36 58.3% 0/21 0.0% 1974 NA +21 phiX2 + 3076 942 941 970 29 AAGTCTGCCGCTGATAAAGGAAAGGATAC HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 AAGTCTGCCGATGATAAAGGAAAGGATAC ..........x.................. 29M 28/29 96.6% 29/36 80.6% 0/29 0.0% 934 NA +22 phiX1 + 2310 2289 2288 2310 22 AGATTGAGTGTGAGGTTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 22 15 14 36 22 AGATTGAGTGTGAGGTTATAAC ...................... 22M 22/22 100.0% 22/36 61.1% 0/22 0.0% 2288 22 +23 phiX2 + 3076 237 236 267 31 TGGTAATGGTGGTTTTCTTCATTGCATTCAG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TGGTAATGGTGGTTTTCTTCATTTCATTCAG .......................x....... 31M 30/31 96.8% 31/36 86.1% 0/31 0.0% 236 NA +24 phiX2 + 3076 1420 1419 1443 24 AGAATCAGCGGTATGGCTCTTCTC HWI-EAS91_1_306UPAAXX + 36 1 0 24 1 0 24 24 AGAATCAGCGGTATGGCTCTTCTC ........................ 24M 24/24 100.0% 24/36 66.7% 0/24 0.0% 1419 NA +25 phiX1 + 2310 2286 2285 2310 25 AAAAGATTGAGTGTGAGGTTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 25 12 11 36 25 AAAAGATTGAGTGTGAGGTTATAAC ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 2285 25 +25 phiX2 + 3076 188 187 212 25 CTAAAGCTACATCGTCAACGTTATA HWI-EAS91_1_306UPAAXX - 36 12 11 36 1 0 25 25 CTAAAGCTACATCGTCAACGTTATA ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 176 NA +25 phiX2 + 3076 2345 2344 2369 25 TGATATTGGTCGTATGGTTCTTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 25 1 0 25 25 TGATATTGGTCGTATGGTTCTTGCT ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 2344 NA +25 phiX2 + 3076 517 516 549 33 ATGGTTTGGTCTAACTTTACCGCTACTAAATGC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 ATGGTTTGGTCAAACTTTACCGCTACTAAATGC ...........x..................... 33M 32/33 97.0% 33/36 91.7% 0/33 0.0% 513 NA +25 phiX2 + 3076 575 574 607 33 TTATTAAAGAGATTATTTGTCTCCAGCCACTTA HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTATTAAAGAGATTATTTTTCTCCAGCCACTTA ..................x.............. 33M 32/33 97.0% 33/36 91.7% 0/33 0.0% 574 NA +26 phiX1 + 2310 1139 1138 1172 34 GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG ..........................x....... 34M 33/34 97.1% 34/36 94.4% 0/34 0.0% 1138 NA +26 phiX1 + 2310 664 663 689 26 AAACGGCCTGTCTCATCATGGAAGGC HWI-EAS91_1_306UPAAXX - 36 11 10 36 1 0 26 26 AAACGGCCTGTCTCATCATGGAAGGC .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 653 NA +26 phiX1 + 2310 664 663 689 26 AAACGGCCTGTCTCATCATGGAAGGC HWI-EAS91_1_306UPAAXX - 36 11 10 36 1 0 26 26 AAACGGCCTGTCTCATCATGGAAGGC .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 653 NA +26 phiX2 + 3076 1472 1471 1497 26 TAATGTCGTCACTGATGCTGCTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 26 1 0 26 26 TAATGTCGTCACTGATGCTGCTTCTG .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 1471 NA +26 phiX2 + 3076 1726 1725 1751 26 GTATCGAGGCTCTTAAACCTGCTATT HWI-EAS91_1_306UPAAXX + 36 1 0 26 1 0 26 26 GTATCGAGGCTCTTAAACCTGCTATT .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 1725 NA +27 phiX1 + 2310 558 557 584 27 GCTTGCGTTTATGGTACGCTGGACTTT HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 GCTTGCGTTTATGGTACGCTGGACTTT ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 557 NA +27 phiX1 + 2310 571 570 605 35 GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT ........x.......................... 35M 34/35 97.1% 35/36 97.2% 0/35 0.0% 570 NA +27 phiX2 + 3076 1911 1910 1937 27 TCTGACGTTCGTGATGAGTTTGTATCT HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 TCTGACGTTCGTGATGAGTTTGTATCT ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 1910 NA +27 phiX2 + 3076 2346 2345 2372 27 GATATTGGTCGTATGGTTCTTGCTGCC HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 GATATTGGTCGTATGGTTCTTGCTGCC ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 2345 NA +27 phiX2 + 3076 2362 2361 2388 27 TTCTTGCTGCCGAGGGTCGCAAGGCTA HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 TTCTTGCTGCCGAGGGTCGCAAGGCTA ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 2361 NA +27 phiX2 + 3076 2457 2456 2491 35 CATTTCCATGCGGTGCACTTTATGCGGACACTTCC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC .................:................. 35M 34/35 97.1% 35/36 97.2% 0/35 0.0% 2455 NA +28 phiX1 + 2310 1626 1625 1661 36 GTGATTACTTCATGCAGCGTTACCATGATGTTATTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT ........................:........... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1625 NA +28 phiX1 + 2310 1982 1981 2017 36 GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT ..............x..................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1981 NA +28 phiX1 + 2310 2148 2147 2183 36 GCGTACTTATTCGCCACCATGATTATGACCAGTGTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT ..........................x......... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2147 NA +28 phiX1 + 2310 2222 2221 2257 36 AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC .............x...................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2221 NA +28 phiX2 + 3076 171 170 206 36 ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC ..........x......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 170 NA +28 phiX2 + 3076 1788 1787 1823 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC ............x....................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1787 NA +28 phiX2 + 3076 1918 1917 1945 28 TTCGTGATGAGTTTGTATCTGTTACTGA HWI-EAS91_1_306UPAAXX + 36 1 0 28 1 0 28 28 TTCGTGATGAGTTTGTATCTGTTACTGA ............................ 28M 28/28 100.0% 28/36 77.8% 0/28 0.0% 1917 NA +28 phiX2 + 3076 2189 2188 2224 36 GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT ...................:................ 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2188 NA +28 phiX2 + 3076 2325 2324 2352 28 GCTTTGCGTGACTATTTTCGTGATATTG HWI-EAS91_1_306UPAAXX + 36 1 0 28 1 0 28 28 GCTTTGCGTGACTATTTTCGTGATATTG ............................ 28M 28/28 100.0% 28/36 77.8% 0/28 0.0% 2324 NA +28 phiX2 + 3076 2327 2326 2362 36 TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT ..........................x......... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2326 NA +28 phiX2 + 3076 2465 2464 2500 36 TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG .........:.......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2464 NA +28 phiX2 + 3076 2507 2506 2542 36 CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA .........x.......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2506 NA +28 phiX2 + 3076 646 645 681 36 TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT .................x.................. 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 645 NA +28 phiX2 + 3076 660 659 695 36 GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT .......................x............ 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 659 NA +28 phiX2 + 3076 789 788 824 36 CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC ............................:....... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 788 NA +29 phiX1 + 2310 598 597 626 29 GCTTTCCTGCTCCTGTTGAGTTTATTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GCTTTCCTGCTCCTGTTGAGTTTATTGCT ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 597 NA +29 phiX2 + 3076 1176 1175 1204 29 CAGAATACGAAAGACCAGGTATATGCACA HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 CAGAATACGAAAGACCAGGTATATGCACA ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 1168 NA +29 phiX2 + 3076 1518 1517 1546 29 GGTATTGATAAAGCTGTTGCCGATACTTG HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GGTATTGATAAAGCTGTTGCCGATACTTG ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 1517 NA +29 phiX2 + 3076 2282 2281 2310 29 GTTGGCTGACGACCGATTAGAGGCGTTTT HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GTTGGCTGACGACCGATTAGAGGCGTTTT ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 2281 NA +29 phiX2 + 3076 3048 3047 3076 29 ATAAAAATGATTGGCGTATCCAACCTGCA HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 ATAAAAATGATTGGCGTATCCAACCTGCA ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 3047 29 +29 phiX2 + 3076 953 952 981 29 TGATAAAGGAAAGGATACTCGTGATTATC HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 TGATAAAGGAAAGGATACTCGTGATTATC ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 945 NA +30 phiX1 + 2310 1112 1111 1141 30 GCTGGCGACTCCTTCGAGATGGACGCCGTT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GCTGGCGACTCCTTCGAGATGGACGCCGTT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1111 NA +30 phiX1 + 2310 1702 1701 1731 30 TCCTTTACTTGTCATGCGCTCTAATCTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TCCTTTACTTGTCATGCGCTCTAATCTCTG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1701 NA +30 phiX1 + 2310 624 623 653 30 GCTGCCGTCATTGCTTATTATGTTCATCCC HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GCTGCCGTCATTGCTTATTATGTTCATCCC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 623 NA +30 phiX1 + 2310 638 637 667 30 TTATTATGTTCATCCCGTCAACATTCAAAC HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TTATTATGTTCATCCCGTCAACATTCAAAC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 637 NA +30 phiX1 + 2310 81 80 110 30 GAATTACTACTGCTTGTTTACGAATTAAAT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GAATTACTACTGCTTGTTTACGAATTAAAT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 80 NA +30 phiX1 + 2310 989 988 1018 30 TGAGGATAAATTATGTCTAATATTCAAACT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TGAGGATAAATTATGTCTAATATTCAAACT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 988 NA +30 phiX2 + 3076 1468 1467 1497 30 TTTCTAATGTCGTCACTGATGCTGCTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TTTCTAATGTCGTCACTGATGCTGCTTCTG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1467 NA +30 phiX2 + 3076 1500 1499 1529 30 GTGGTTGATATTTTTCATGGTATTGATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GTGGTTGATATTTTTCATGGTATTGATAAA .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1499 NA +30 phiX2 + 3076 1863 1862 1892 30 GTTGAGTTCGATAATGGTGATATGTATGTT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GTTGAGTTCGATAATGGTGATATGTATGTT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1862 NA +30 phiX2 + 3076 2020 2019 2055 36 GCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG ..............X.X................... 36M 34/34 100.0% 36/36 100.0% 0/36 0.0% 2019 NA +30 phiX2 + 3076 2444 2443 2473 30 TAATGGCCGTCTTCATTTCCATGCGGTGCA HWI-EAS91_1_306UPAAXX - 36 1 0 30 7 6 36 30 TAATGGCCGTCTTCATTTCCATGCGGTGCA .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 2443 NA +30 phiX2 + 3076 502 501 531 30 GTTTATGTTGGTTTCATGGTTTGGTCTAAC HWI-EAS91_1_306UPAAXX - 36 7 6 36 1 0 30 30 GTTTATGTTGGTTTCATGGTTTGGTCTAAC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 495 NA +30 phiX2 + 3076 858 857 887 30 GGTAAAGGACTTCTTGAAGGTACGTTGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GGTAAAGGACTTCTTGAAGGTACGTTGCAG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 857 NA +31 phiX1 + 2310 1346 1345 1376 31 GATACCAATAAAATCCCTAAGCATTTGTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GATACCAATAAAATCCCTAAGCATTTGTTTC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1345 NA +31 phiX1 + 2310 1807 1806 1837 31 TAAACATTCTGTGCCGCGTTTCTTTGTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TAAACATTCTGTGCCGCGTTTCTTTGTTCCT ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1806 NA +31 phiX2 + 3076 1022 1021 1052 31 TGGTGCTGATGCTTCCTCTGCTGGTATGGTT HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TGGTGCTGATGCTTCCTCTGCTGGTATGGTT ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1021 NA +31 phiX2 + 3076 198 197 228 31 ATCGTCAACGTTATATTTTGATAGTTTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 ATCGTCAACGTTATATTTTGATAGTTTGACG ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 197 NA +31 phiX2 + 3076 2064 2063 2094 31 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTG ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2063 NA +31 phiX2 + 3076 2443 2442 2473 31 CTAATGGCCGTCTTCATTTCCATGCGGTGCA HWI-EAS91_1_306UPAAXX - 36 1 0 31 6 5 36 31 CTAATGGCCGTCTTCATTTCCATGCGGTGCA ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2442 NA +31 phiX2 + 3076 2705 2704 2735 31 TAAATACGTTAACAAAAAGTCAGATATGGAC HWI-EAS91_1_306UPAAXX - 36 6 5 36 1 0 31 31 TAAATACGTTAACAAAAAGTCAGATATGGAC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2699 NA +31 phiX2 + 3076 331 330 361 31 GCCGACCCTAAATTTTTTGCCTGTTTGGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GCCGACCCTAAATTTTTTGCCTGTTTGGTTC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 330 NA +32 phiX1 + 2310 1 0 32 32 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA HWI-EAS91_1_306UPAAXX - 36 5 4 36 1 0 32 32 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% -4 -32 +32 phiX1 + 2310 1266 1265 1297 32 GTGTTAATGCCACTCCTCTCCCGACTGTTAAC HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 GTGTTAATGCCACTCCTCTCCCGACTGTTAAC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 1265 NA +32 phiX1 + 2310 801 800 832 32 GCAGAAGAAAACGTGCGTCAAAAATTACGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 32 5 4 36 32 GCAGAAGAAAACGTGCGTCAAAAATTACGTGC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 800 NA +32 phiX2 + 3076 1380 1379 1411 32 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCA HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 1379 NA +32 phiX2 + 3076 2145 2144 2176 32 GGTATTAAGGATGAGTGTTCAAGATTGCTGGA HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 GGTATTAAGGATGAGTGTTCAAGATTGCTGGA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 2144 NA +32 phiX2 + 3076 352 351 383 32 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCC HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 351 NA +33 phiX1 + 2310 1203 1202 1235 33 TTACTTTTTATGTCCCTCATCGTCACGTTTATG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTACTTTTTATGTCCCTCATCGTCACGTTTATG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1202 NA +33 phiX1 + 2310 1313 1312 1345 33 GACCATGCCGCTTTTCTTGGCACGATTAACCCT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GACCATGCCGCTTTTCTTGGCACGATTAACCCT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1312 NA +33 phiX1 + 2310 1379 1378 1411 33 GGTTATTTGAATATCTATAACAACTATTTTAAA HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGTTATTTGAATATCTATAACAACTATTTTAAA ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1378 NA +33 phiX1 + 2310 1544 1543 1576 33 CGCCAAATGACGACTTCTACCACATCTATTGAC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 CGCCAAATGACGACTTCTACCACATCTATTGAC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1540 NA +33 phiX1 + 2310 636 635 668 33 GCTTATTATGTTCATCCCGTCAACATTCAAACG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCTTATTATGTTCATCCCGTCAACATTCAAACG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 635 NA +33 phiX2 + 3076 1470 1469 1502 33 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1469 NA +33 phiX2 + 3076 1662 1661 1694 33 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1661 NA +33 phiX2 + 3076 1864 1863 1896 33 TTGAGTTCGATAATGGTGATATGTATGTTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTGAGTTCGATAATGGTGATATGTATGTTGACG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1863 NA +33 phiX2 + 3076 2253 2252 2285 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 2252 NA +33 phiX2 + 3076 2606 2605 2638 33 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 2605 NA +33 phiX2 + 3076 345 344 377 33 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 344 NA +33 phiX2 + 3076 428 427 460 33 GCCATGATGGTGGTTATTATACCGTCAAGGACT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCCATGATGGTGGTTATTATACCGTCAAGGACT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 427 NA +33 phiX2 + 3076 572 571 604 33 AGGTTATTAAAGAGATTATTTGTCTCCAGCCAC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 AGGTTATTAAAGAGATTATTTGTCTCCAGCCAC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 568 NA +33 phiX2 + 3076 884 883 916 33 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 883 NA +34 phiX1 + 2310 1180 1179 1213 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1179 NA +34 phiX1 + 2310 1180 1179 1213 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1179 NA +34 phiX1 + 2310 1254 1253 1287 34 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1251 NA +34 phiX1 + 2310 320 319 353 34 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 319 NA +34 phiX1 + 2310 582 581 615 34 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 581 NA +34 phiX2 + 3076 1826 1825 1859 34 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1825 NA +34 phiX2 + 3076 201 200 234 34 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 200 NA +34 phiX2 + 3076 2034 2033 2067 34 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2031 NA +34 phiX2 + 3076 2174 2173 2207 34 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTT HWI-EAS91_1_306UPAAXX - 36 1 0 34 3 2 36 34 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2173 NA +34 phiX2 + 3076 2296 2295 2329 34 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2295 NA +34 phiX2 + 3076 2475 2474 2508 34 TTTATGCGGACACTTCCTACAGGTAGCGTTGACC HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 TTTATGCGGACACTTCCTACAGGTAGCGTTGACC .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2472 NA +35 phiX1 + 2310 10 9 44 35 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 8 NA +35 phiX1 + 2310 1045 1044 1079 35 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1044 NA 35 phiX1 + 2310 1067 1066 1101 35 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GGTCAGATTGGTCGTCTTATTACCATTTCAACTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1065 NA -36 phiX1 + 2310 1788 1787 1823 36 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1787 NA +35 phiX1 + 2310 1093 1092 1127 35 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1092 NA +35 phiX1 + 2310 1165 1164 1199 35 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1163 NA +35 phiX1 + 2310 1172 1171 1206 35 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1170 NA +35 phiX1 + 2310 1249 1248 1283 35 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1247 NA +35 phiX1 + 2310 1274 1273 1308 35 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1272 NA +35 phiX1 + 2310 1294 1293 1328 35 TAACACTACTGGTTATATTGACCATGCCGCTTTTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TAACACTACTGGTTATATTGACCATGCCGCTTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1292 NA +35 phiX1 + 2310 1508 1507 1542 35 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1506 NA +35 phiX1 + 2310 1521 1520 1555 35 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1520 NA +35 phiX1 + 2310 1552 1551 1586 35 GACGACTTCTACCACATCTATTGACATTATGGGTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GACGACTTCTACCACATCTATTGACATTATGGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1550 NA +35 phiX1 + 2310 1579 1578 1613 35 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1577 NA +35 phiX1 + 2310 1613 1612 1647 35 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1611 NA +35 phiX1 + 2310 1877 1876 1911 35 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1875 NA +35 phiX1 + 2310 1940 1939 1974 35 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1938 NA +35 phiX1 + 2310 195 194 229 35 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 194 NA +35 phiX1 + 2310 204 203 238 35 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 203 NA +35 phiX1 + 2310 2112 2111 2146 35 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2110 NA +35 phiX1 + 2310 2212 2211 2246 35 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2211 NA +35 phiX1 + 2310 2254 2253 2288 35 GACCACTCGCGATTCAATCATGACTTCGTGATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GACCACTCGCGATTCAATCATGACTTCGTGATAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2253 NA +35 phiX1 + 2310 358 357 392 35 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 357 NA +35 phiX1 + 2310 411 410 445 35 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 410 NA +35 phiX1 + 2310 521 520 555 35 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 520 NA +35 phiX1 + 2310 527 526 561 35 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 526 NA +35 phiX1 + 2310 540 539 574 35 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 538 NA +35 phiX1 + 2310 614 613 648 35 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 613 NA +35 phiX1 + 2310 646 645 680 35 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 645 NA +35 phiX1 + 2310 680 679 714 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 678 NA +35 phiX1 + 2310 680 679 714 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 678 NA +35 phiX1 + 2310 789 788 823 35 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 788 NA +35 phiX1 + 2310 798 797 832 35 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 796 NA +35 phiX2 + 3076 11 10 45 35 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 10 NA +35 phiX2 + 3076 1124 1123 1158 35 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1122 NA +35 phiX2 + 3076 1498 1497 1532 35 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1497 NA +35 phiX2 + 3076 1507 1506 1541 35 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1506 NA +35 phiX2 + 3076 1524 1523 1558 35 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1523 NA +35 phiX2 + 3076 1542 1541 1576 35 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1540 NA +35 phiX2 + 3076 157 156 191 35 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 155 NA +35 phiX2 + 3076 1778 1777 1812 35 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1777 NA +35 phiX2 + 3076 1888 1887 1922 35 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1886 NA +35 phiX2 + 3076 1925 1924 1959 35 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1924 NA +35 phiX2 + 3076 1985 1984 2019 35 CCCCCAACTTGATATTAATAACACTATAGACCACC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCCCCAACTTGATATTAATAACACTATAGACCACC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1983 NA +35 phiX2 + 3076 1997 1996 2031 35 TATTAATAACACTATAGACCACCGCCCCGAAGGGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATTAATAACACTATAGACCACCGCCCCGAAGGGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1996 NA +35 phiX2 + 3076 2222 2221 2256 35 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2220 NA +35 phiX2 + 3076 2277 2276 2311 35 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2275 NA +35 phiX2 + 3076 2309 2308 2343 35 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2308 NA +35 phiX2 + 3076 2348 2347 2382 35 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2347 NA +35 phiX2 + 3076 2349 2348 2383 35 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2347 NA +35 phiX2 + 3076 2357 2356 2391 35 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2356 NA +35 phiX2 + 3076 2578 2577 2612 35 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2576 NA +35 phiX2 + 3076 2601 2600 2635 35 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2600 NA +35 phiX2 + 3076 2816 2815 2850 35 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2814 NA +35 phiX2 + 3076 2858 2857 2892 35 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2856 NA +35 phiX2 + 3076 2881 2880 2915 35 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2880 NA +35 phiX2 + 3076 393 392 427 35 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 391 NA +35 phiX2 + 3076 420 419 454 35 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 419 NA +35 phiX2 + 3076 433 432 467 35 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 431 NA +35 phiX2 + 3076 440 439 474 35 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 439 NA +35 phiX2 + 3076 453 452 487 35 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 451 NA +35 phiX2 + 3076 502 501 536 35 GTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 500 NA +35 phiX2 + 3076 533 532 567 35 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 532 NA +35 phiX2 + 3076 547 546 581 35 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 546 NA +35 phiX2 + 3076 597 596 631 35 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 595 NA +35 phiX2 + 3076 654 653 688 35 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 653 NA +35 phiX2 + 3076 735 734 769 35 GCTACCGATAACAATACTGTAGGCATGGGTGATGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCTACCGATAACAATACTGTAGGCATGGGTGATGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 733 NA +35 phiX2 + 3076 756 755 790 35 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 755 NA +35 phiX2 + 3076 816 815 850 35 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 814 NA +36 phiX1 + 2310 1002 1001 1037 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1001 NA +36 phiX1 + 2310 1002 1001 1037 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1001 NA +36 phiX1 + 2310 1012 1011 1047 36 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1011 NA +36 phiX1 + 2310 1014 1013 1049 36 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1013 NA +36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA +36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA +36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA +36 phiX1 + 2310 1091 1090 1126 36 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1090 NA +36 phiX1 + 2310 1115 1114 1150 36 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1114 NA +36 phiX1 + 2310 1116 1115 1151 36 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1115 NA +36 phiX1 + 2310 1144 1143 1179 36 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1143 NA +36 phiX1 + 2310 1155 1154 1190 36 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1154 NA 36 phiX1 + 2310 1193 1192 1228 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1192 NA -36 phiX1 + 2310 1590 1589 1625 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1589 NA -36 phiX1 + 2310 1701 1700 1736 36 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1700 NA -36 phiX1 + 2310 1683 1682 1718 36 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1682 NA -36 phiX1 + 2310 1665 1664 1700 36 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1664 NA -36 phiX1 + 2310 513 512 548 36 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 512 NA +36 phiX1 + 2310 1193 1192 1228 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1192 NA +36 phiX1 + 2310 1207 1206 1242 36 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1206 NA +36 phiX1 + 2310 1214 1213 1249 36 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1213 NA +36 phiX1 + 2310 1224 1223 1259 36 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1223 NA 36 phiX1 + 2310 1229 1228 1264 36 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTTATGGTGAACAGTGGATTAAGTTCATGAAGGAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1228 NA -36 phiX1 + 2310 615 614 650 36 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 614 NA -36 phiX1 + 2310 257 256 292 36 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 256 NA -36 phiX1 + 2310 1888 1887 1923 36 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1887 NA -36 phiX1 + 2310 1828 1827 1863 36 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1827 NA -36 phiX1 + 2310 22 21 57 36 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 21 NA -35 phiX1 + 2310 358 357 392 35 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATGCTGTTCAACCACTAATAGGTAAGAAATCATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 357 NA -36 phiX1 + 2310 1775 1774 1810 36 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1774 NA -36 phiX1 + 2310 1554 1553 1589 36 CGACTTCTACCACATCTATTGACATTATGGGTCTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGACTTCTACCACATCTATTGACATTATGGGTCTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1553 NA -36 phiX1 + 2310 1002 1001 1037 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1001 NA +36 phiX1 + 2310 1242 1241 1277 36 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1241 NA +36 phiX1 + 2310 1249 1248 1284 36 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1248 NA +36 phiX1 + 2310 1252 1251 1287 36 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1251 NA 36 phiX1 + 2310 1265 1264 1300 36 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1264 NA 36 phiX1 + 2310 1332 1331 1367 36 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCACGATTAACCCTGATACCAATAAAATCCCTAAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1331 NA +36 phiX1 + 2310 1364 1363 1399 36 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1363 NA +36 phiX1 + 2310 1461 1460 1496 36 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1460 NA +36 phiX1 + 2310 1514 1513 1549 36 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1513 NA +36 phiX1 + 2310 1522 1521 1557 36 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1521 NA +36 phiX1 + 2310 1529 1528 1564 36 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1528 NA +36 phiX1 + 2310 1536 1535 1571 36 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1535 NA +36 phiX1 + 2310 154 153 189 36 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 153 NA +36 phiX1 + 2310 1545 1544 1580 36 GCCAAATGACGACTTCTACCACATCTATTGACATTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCCAAATGACGACTTCTACCACATCTATTGACATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1544 NA +36 phiX1 + 2310 1554 1553 1589 36 CGACTTCTACCACATCTATTGACATTATGGGTCTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGACTTCTACCACATCTATTGACATTATGGGTCTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1553 NA +36 phiX1 + 2310 156 155 191 36 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 155 NA +36 phiX1 + 2310 157 156 192 36 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 156 NA +36 phiX1 + 2310 1575 1574 1610 36 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1574 NA +36 phiX1 + 2310 1579 1578 1614 36 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1578 NA +36 phiX1 + 2310 1580 1579 1615 36 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1579 NA +36 phiX1 + 2310 1582 1581 1617 36 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1581 NA +36 phiX1 + 2310 1587 1586 1622 36 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1586 NA +36 phiX1 + 2310 1588 1587 1623 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1587 NA +36 phiX1 + 2310 1588 1587 1623 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1587 NA +36 phiX1 + 2310 1590 1589 1625 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1589 NA +36 phiX1 + 2310 1590 1589 1625 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1589 NA +36 phiX1 + 2310 161 160 196 36 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 160 NA +36 phiX1 + 2310 1655 1654 1690 36 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1654 NA +36 phiX1 + 2310 1657 1656 1692 36 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1656 NA +36 phiX1 + 2310 1662 1661 1697 36 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1661 NA +36 phiX1 + 2310 1665 1664 1700 36 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTTGGAGGTAAAACCTCTTATGACGCTGACAACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1664 NA 36 phiX1 + 2310 1670 1669 1705 36 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGAGGTAAAACCTCTTATGACGCTGACAACCGTCCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1669 NA +36 phiX1 + 2310 1674 1673 1709 36 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1673 NA +36 phiX1 + 2310 1683 1682 1718 36 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATGACGCTGACAACCGTCCTTTACTTGTCATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1682 NA +36 phiX1 + 2310 1690 1689 1725 36 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1689 NA +36 phiX1 + 2310 1701 1700 1736 36 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1700 NA +36 phiX1 + 2310 1707 1706 1742 36 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1706 NA +36 phiX1 + 2310 1719 1718 1754 36 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1718 NA +36 phiX1 + 2310 1721 1720 1756 36 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1720 NA +36 phiX1 + 2310 1728 1727 1763 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1727 NA +36 phiX1 + 2310 1728 1727 1763 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1727 NA +36 phiX1 + 2310 1734 1733 1769 36 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1733 NA +36 phiX1 + 2310 1764 1763 1799 36 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1763 NA +36 phiX1 + 2310 177 176 212 36 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 176 NA +36 phiX1 + 2310 1775 1774 1810 36 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1774 NA +36 phiX1 + 2310 1788 1787 1823 36 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCGTGTTCAACAGACCTATAAACATTCTGTGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1787 NA +36 phiX1 + 2310 1800 1799 1835 36 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1799 NA +36 phiX1 + 2310 1828 1827 1863 36 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1827 NA +36 phiX1 + 2310 1843 1842 1878 36 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1842 NA +36 phiX1 + 2310 1852 1851 1887 36 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1851 NA +36 phiX1 + 2310 1867 1866 1902 36 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1866 NA +36 phiX1 + 2310 1888 1887 1923 36 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1887 NA +36 phiX1 + 2310 1946 1945 1981 36 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1945 NA +36 phiX1 + 2310 1948 1947 1983 36 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1947 NA +36 phiX1 + 2310 1954 1953 1989 36 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1953 NA +36 phiX1 + 2310 1957 1956 1992 36 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1956 NA +36 phiX1 + 2310 1974 1973 2009 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1973 NA +36 phiX1 + 2310 2004 2003 2039 36 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2003 NA +36 phiX1 + 2310 2059 2058 2094 36 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2058 NA +36 phiX1 + 2310 206 205 241 36 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 205 NA +36 phiX1 + 2310 2071 2070 2106 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA +36 phiX1 + 2310 2071 2070 2106 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA +36 phiX1 + 2310 2099 2098 2134 36 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2098 NA +36 phiX1 + 2310 2100 2099 2135 36 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2099 NA +36 phiX1 + 2310 2116 2115 2151 36 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2115 NA +36 phiX1 + 2310 2128 2127 2163 36 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2127 NA +36 phiX1 + 2310 2154 2153 2189 36 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2153 NA +36 phiX1 + 2310 2160 2159 2195 36 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2159 NA +36 phiX1 + 2310 2175 2174 2210 36 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2174 NA +36 phiX1 + 2310 22 21 57 36 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAGAAGTTAACACTTTCGGATATTTCTGATGAGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 21 NA +36 phiX1 + 2310 220 219 255 36 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 219 NA +36 phiX1 + 2310 2217 2216 2252 36 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2216 NA +36 phiX1 + 2310 2225 2224 2260 36 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2224 NA +36 phiX1 + 2310 2239 2238 2274 36 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2238 NA +36 phiX1 + 2310 227 226 262 36 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 226 NA +36 phiX1 + 2310 229 228 264 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 228 NA +36 phiX1 + 2310 231 230 266 36 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 230 NA +36 phiX1 + 2310 242 241 277 36 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 241 NA +36 phiX1 + 2310 257 256 292 36 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCACGTTCGTCAAGGACTGGTTTAGATATGAGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 256 NA +36 phiX1 + 2310 286 285 321 36 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 285 NA +36 phiX1 + 2310 289 288 324 36 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 288 NA +36 phiX1 + 2310 305 304 340 36 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 304 NA +36 phiX1 + 2310 318 317 353 36 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 317 NA +36 phiX1 + 2310 332 331 367 36 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 331 NA +36 phiX1 + 2310 333 332 368 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 332 NA +36 phiX1 + 2310 338 337 373 36 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 337 NA +36 phiX1 + 2310 339 338 374 36 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 338 NA +36 phiX1 + 2310 348 347 383 36 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 347 NA +36 phiX1 + 2310 349 348 384 36 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 348 NA +36 phiX1 + 2310 379 378 414 36 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA +36 phiX1 + 2310 388 387 423 36 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 387 NA +36 phiX1 + 2310 409 408 444 36 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 408 NA +36 phiX1 + 2310 441 440 476 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 440 NA +36 phiX1 + 2310 441 440 476 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 440 NA +36 phiX1 + 2310 485 484 520 36 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 484 NA +36 phiX1 + 2310 496 495 531 36 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 495 NA +36 phiX1 + 2310 513 512 548 36 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 512 NA +36 phiX1 + 2310 521 520 556 36 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 520 NA +36 phiX1 + 2310 524 523 559 36 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 523 NA +36 phiX1 + 2310 533 532 568 36 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 532 NA +36 phiX1 + 2310 54 53 89 36 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 53 NA +36 phiX1 + 2310 555 554 590 36 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 554 NA +36 phiX1 + 2310 557 556 592 36 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 556 NA +36 phiX1 + 2310 574 573 609 36 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 573 NA +36 phiX1 + 2310 584 583 619 36 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 583 NA +36 phiX1 + 2310 611 610 646 36 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 610 NA +36 phiX1 + 2310 613 612 648 36 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 612 NA +36 phiX1 + 2310 615 614 650 36 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 614 NA +36 phiX1 + 2310 632 631 667 36 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 631 NA +36 phiX1 + 2310 635 634 670 36 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 634 NA +36 phiX1 + 2310 636 635 671 36 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 635 NA 36 phiX1 + 2310 640 639 675 36 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 639 NA -21 phiX1 + 2310 1 0 21 21 GAGTTTTATCGCTTCCATGAC HWI-EAS91_1_306UPAAXX - 36 16 15 36 1 0 21 21 GAGTTTTATCGCTTCCATGAC ..................... 21M 21/21 100.0% 21/36 58.3% 0/21 0.0% -15 -21 -36 phiX1 + 2310 1674 1673 1709 36 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTAAAACCTCTTATGACGCTGACAACCGTCCTTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1673 NA -36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA -36 phiX1 + 2310 1115 1114 1150 36 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1114 NA -33 phiX1 + 2310 636 635 668 33 GCTTATTATGTTCATCCCGTCAACATTCAAACG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCTTATTATGTTCATCCCGTCAACATTCAAACG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 635 NA -26 phiX1 + 2310 1139 1138 1172 34 GTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GTTGGCGCTCTCCGTCTTTCTCCATTTCGTCGTG ..........................x....... 34M 33/34 97.1% 34/36 94.4% 0/34 0.0% 1138 NA +36 phiX1 + 2310 660 659 695 36 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 659 NA +36 phiX1 + 2310 72 71 107 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 71 NA +36 phiX1 + 2310 727 726 762 36 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 726 NA +36 phiX1 + 2310 772 771 807 36 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 771 NA 36 phiX1 + 2310 852 851 887 36 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 851 NA -36 phiX1 + 2310 632 631 667 36 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTGCTTATTATGTTCATCCCGTCAACATTCAAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 631 NA -36 phiX1 + 2310 1719 1718 1754 36 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCTAATCTCTGGGCATCTGGCTATGATGTTGATG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1718 NA -29 phiX1 + 2310 598 597 626 29 GCTTTCCTGCTCCTGTTGAGTTTATTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GCTTTCCTGCTCCTGTTGAGTTTATTGCT ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 597 NA -36 phiX1 + 2310 379 378 414 36 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTAAGAAATCATGAGTCAAGTTACTGAACAATCCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA -36 phiX1 + 2310 2160 2159 2195 36 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCACCATGATTATGACCAGTGTTTCCAGTCCGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2159 NA -35 phiX1 + 2310 1508 1507 1542 35 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1506 NA -36 phiX1 + 2310 635 634 670 36 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGCTTATTATGTTCATCCCGTCAACATTCAAACGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 634 NA -35 phiX1 + 2310 1294 1293 1328 35 TAACACTACTGGTTATATTGACCATGCCGCTTTTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TAACACTACTGGTTATATTGACCATGCCGCTTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1292 NA -36 phiX1 + 2310 772 771 807 36 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGCAGGAAACACTGACGTTCTTACTGACGCAGAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 771 NA -36 phiX1 + 2310 1224 1223 1259 36 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCACGTTTATGGTGAACAGTGGATTAAGTTCATGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1223 NA -33 phiX1 + 2310 1544 1543 1576 33 CGCCAAATGACGACTTCTACCACATCTATTGAC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 CGCCAAATGACGACTTCTACCACATCTATTGAC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1540 NA -35 phiX1 + 2310 204 203 238 35 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATTCTGTCAAAAACTGACGCGTTGGATGAGGAGA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 203 NA -36 phiX1 + 2310 332 331 367 36 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 331 NA -14 phiX1 + 2310 2192 2191 2213 22 GTTCAGTTGTTGCAGTGGAATA HWI-EAS91_1_306UPAAXX + 36 1 0 22 1 0 22 22 GTTCAGTTGTTGCATTGGAATA ..............x....... 22M 21/22 95.5% 22/36 61.1% 0/22 0.0% 2191 NA -36 phiX1 + 2310 1193 1192 1228 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTAGACATTTTTACTTTTTATGTCCCTCATCGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1192 NA -36 phiX1 + 2310 157 156 192 36 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 156 NA -36 phiX1 + 2310 1091 1090 1126 36 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1090 NA -35 phiX1 + 2310 798 797 832 35 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GACGCAGAAGAAAACGTGCGTCAAAAATTACGTGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 796 NA -36 phiX1 + 2310 1655 1654 1690 36 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTATTTCTTCATTTGGAGGTAAAACCTCTTATGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1654 NA -35 phiX1 + 2310 1249 1248 1283 35 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1247 NA -30 phiX1 + 2310 81 80 110 30 GAATTACTACTGCTTGTTTACGAATTAAAT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GAATTACTACTGCTTGTTTACGAATTAAAT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 80 NA -35 phiX1 + 2310 789 788 823 35 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 788 NA -36 phiX1 + 2310 305 304 340 36 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 304 NA -36 phiX1 + 2310 1461 1460 1496 36 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1460 NA -36 phiX1 + 2310 220 219 255 36 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 219 NA -32 phiX1 + 2310 1266 1265 1297 32 GTGTTAATGCCACTCCTCTCCCGACTGTTAAC HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 GTGTTAATGCCACTCCTCTCCCGACTGTTAAC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 1265 NA -35 phiX1 + 2310 1172 1171 1206 35 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GGCCTTGCTATTGACTCTACTGTAGACATTTTTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1170 NA -36 phiX1 + 2310 636 635 671 36 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTTATTATGTTCATCCCGTCAACATTCAAACGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 635 NA -36 phiX1 + 2310 1014 1013 1049 36 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1013 NA -28 phiX1 + 2310 2148 2147 2183 36 GCGTACTTATTCGCCACCATGATTATGACCAGTGTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGTACTTATTCGCCACCATGATTATTACCAGTGTT ..........................x......... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2147 NA -36 phiX1 + 2310 1590 1589 1625 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCTGCTTATGCTAATTTGCATACTGACCAAGAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1589 NA -27 phiX1 + 2310 571 570 605 35 GTACGCTGGACTTTGTGGGATACCCTCGCTTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTACGCTGTACTTTGTGGGATACCCTCGCTTTCCT ........x.......................... 35M 34/35 97.1% 35/36 97.2% 0/35 0.0% 570 NA -36 phiX1 + 2310 242 241 277 36 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 241 NA -36 phiX1 + 2310 338 337 373 36 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGGATTACTATCTGAGTCCGATGCTGTTCAACCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 337 NA -30 phiX1 + 2310 1112 1111 1141 30 GCTGGCGACTCCTTCGAGATGGACGCCGTT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GCTGGCGACTCCTTCGAGATGGACGCCGTT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1111 NA -34 phiX1 + 2310 1254 1253 1287 34 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 TCATGAAGGATGGTGTTAATGCCACTCCTCTCCC .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1251 NA -36 phiX1 + 2310 348 347 383 36 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 347 NA -35 phiX1 + 2310 1552 1551 1586 35 GACGACTTCTACCACATCTATTGACATTATGGGTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GACGACTTCTACCACATCTATTGACATTATGGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1550 NA -36 phiX1 + 2310 1764 1763 1799 36 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1763 NA -36 phiX1 + 2310 1529 1528 1564 36 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGACTGAGCTTTCTCGCCAAATGACGACTTCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1528 NA -36 phiX1 + 2310 177 176 212 36 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTTGCGACCTTTCGCCATCAACTAACGATTCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 176 NA -36 phiX1 + 2310 156 155 191 36 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 155 NA -36 phiX1 + 2310 227 226 262 36 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 226 NA -36 phiX1 + 2310 574 573 609 36 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 573 NA -34 phiX1 + 2310 582 581 615 34 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTG .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 581 NA -26 phiX1 + 2310 664 663 689 26 AAACGGCCTGTCTCATCATGGAAGGC HWI-EAS91_1_306UPAAXX - 36 11 10 36 1 0 26 26 AAACGGCCTGTCTCATCATGGAAGGC .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 653 NA -36 phiX1 + 2310 1144 1143 1179 36 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1143 NA -36 phiX1 + 2310 1514 1513 1549 36 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1513 NA -36 phiX1 + 2310 1657 1656 1692 36 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATTTCTTCATTTGGAGGTAAAACCTCTTATGACGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1656 NA -36 phiX1 + 2310 2071 2070 2106 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA -28 phiX1 + 2310 1626 1625 1661 36 GTGATTACTTCATGCAGCGTTACCATGATGTTATTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGATTACTTCATGCAGCGTTACCGTGATGTTATTT ........................:........... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1625 NA -28 phiX1 + 2310 1982 1981 2017 36 GAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAAATTTCTATGAATGATGTTTTCCGTTCTGGTGAT ..............x..................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1981 NA -36 phiX1 + 2310 2217 2216 2252 36 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGTTAAATTTAATGTGACCGTTTATCGCAATCTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2216 NA -36 phiX1 + 2310 1690 1689 1725 36 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1689 NA -36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA -35 phiX1 + 2310 1521 1520 1555 35 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1520 NA +36 phiX1 + 2310 900 899 935 36 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 899 NA +36 phiX1 + 2310 910 909 945 36 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 909 NA 36 phiX1 + 2310 945 944 980 36 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 944 NA -36 phiX1 + 2310 1575 1574 1610 36 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1574 NA -36 phiX1 + 2310 2099 2098 2134 36 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2098 NA -36 phiX1 + 2310 524 523 559 36 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 523 NA -36 phiX1 + 2310 1252 1251 1287 36 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1251 NA -26 phiX1 + 2310 664 663 689 26 AAACGGCCTGTCTCATCATGGAAGGC HWI-EAS91_1_306UPAAXX - 36 11 10 36 1 0 26 26 AAACGGCCTGTCTCATCATGGAAGGC .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 653 NA -36 phiX1 + 2310 1116 1115 1151 36 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1115 NA -36 phiX1 + 2310 613 612 648 36 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 612 NA -36 phiX1 + 2310 289 288 324 36 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCACATTTTGTTCATGGTAGAGATTCTCTTGTTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 288 NA -31 phiX1 + 2310 1346 1345 1376 31 GATACCAATAAAATCCCTAAGCATTTGTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GATACCAATAAAATCCCTAAGCATTTGTTTC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1345 NA -36 phiX1 + 2310 1800 1799 1835 36 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1799 NA -33 phiX1 + 2310 1203 1202 1235 33 TTACTTTTTATGTCCCTCATCGTCACGTTTATG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTACTTTTTATGTCCCTCATCGTCACGTTTATG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1202 NA -30 phiX1 + 2310 624 623 653 30 GCTGCCGTCATTGCTTATTATGTTCATCCC HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GCTGCCGTCATTGCTTATTATGTTCATCCC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 623 NA -35 phiX1 + 2310 1877 1876 1911 35 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCGCCTACTGCGACTAAAGAGATTCAGTACCTTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1875 NA -36 phiX1 + 2310 1214 1213 1249 36 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1213 NA -27 phiX1 + 2310 558 557 584 27 GCTTGCGTTTATGGTACGCTGGACTTT HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 GCTTGCGTTTATGGTACGCTGGACTTT ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 557 NA -35 phiX1 + 2310 2254 2253 2288 35 GACCACTCGCGATTCAATCATGACTTCGTGATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GACCACTCGCGATTCAATCATGACTTCGTGATAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2253 NA -28 phiX1 + 2310 2222 2221 2257 36 AAATTTAATGTGACCGTTTATCGCAATCTGCCGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAATTTAATGTGAACGTTTATCGCAATCTGCCGACC .............x...................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2221 NA -35 phiX1 + 2310 646 645 680 35 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCATCCCGTCAACATTCAAACGGCCTGTCTCATC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 645 NA -36 phiX1 + 2310 1364 1363 1399 36 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGCATTTGTTTCAGGGTTATTTGAATATCTATAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1363 NA -35 phiX1 + 2310 1613 1612 1647 35 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACTGACCAAGAACGTGATTACTTCATGCAGCGTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1611 NA -35 phiX1 + 2310 1045 1044 1079 35 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1044 NA -36 phiX1 + 2310 1588 1587 1623 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1587 NA -36 phiX1 + 2310 339 338 374 36 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGATTACTATCTGAGTCCGATGCTGTTCAACCACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 338 NA -36 phiX1 + 2310 1946 1945 1981 36 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1945 NA -36 phiX1 + 2310 727 726 762 36 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 726 NA -36 phiX1 + 2310 555 554 590 36 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 554 NA -36 phiX1 + 2310 485 484 520 36 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGATTTCGATTTTCTGACGAGTAACAAAGTTTGGAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 484 NA -36 phiX1 + 2310 318 317 353 36 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTGACATTTTAAAAGAGCGTGGATTACTATCTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 317 NA -36 phiX1 + 2310 910 909 945 36 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 909 NA -33 phiX1 + 2310 1379 1378 1411 33 GGTTATTTGAATATCTATAACAACTATTTTAAA HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGTTATTTGAATATCTATAACAACTATTTTAAA ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1378 NA -36 phiX1 + 2310 1843 1842 1878 36 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1842 NA -36 phiX1 + 2310 1082 1081 1117 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1081 NA -36 phiX1 + 2310 1728 1727 1763 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1727 NA -36 phiX1 + 2310 2225 2224 2260 36 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTAATGTGACCGTTTATCGCAATCTGCCGACCACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2224 NA -36 phiX1 + 2310 2059 2058 2094 36 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2058 NA -36 phiX1 + 2310 388 387 423 36 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCATGAGTCAAGTTACTGAACAATCCGTACGTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 387 NA -36 phiX1 + 2310 2128 2127 2163 36 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2127 NA -36 phiX1 + 2310 154 153 189 36 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 153 NA -35 phiX1 + 2310 411 410 445 35 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 410 NA -35 phiX1 + 2310 521 520 555 35 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 520 NA -36 phiX1 + 2310 1662 1661 1697 36 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTCATTTGGAGGTAAAACCTCTTATGACGCTGACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1661 NA -36 phiX1 + 2310 533 532 568 36 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 532 NA -35 phiX1 + 2310 195 194 229 35 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCAACTAACGATTCTGTCAAAAACTGACGCGTTGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 194 NA -36 phiX1 + 2310 2239 2238 2274 36 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATCGCAATCTGCCGACCACTCGCGATTCAATCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2238 NA -33 phiX1 + 2310 1313 1312 1345 33 GACCATGCCGCTTTTCTTGGCACGATTAACCCT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GACCATGCCGCTTTTCTTGGCACGATTAACCCT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1312 NA -36 phiX1 + 2310 1545 1544 1580 36 GCCAAATGACGACTTCTACCACATCTATTGACATTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCCAAATGACGACTTCTACCACATCTATTGACATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1544 NA -36 phiX1 + 2310 557 556 592 36 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 556 NA -36 phiX1 + 2310 1249 1248 1284 36 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1248 NA -35 phiX1 + 2310 614 613 648 35 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGAGTTTATTGCTGCCGTCATTGCTTATTATGTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 613 NA -36 phiX1 + 2310 206 205 241 36 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 205 NA -30 phiX1 + 2310 1702 1701 1731 30 TCCTTTACTTGTCATGCGCTCTAATCTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TCCTTTACTTGTCATGCGCTCTAATCTCTG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1701 NA -36 phiX1 + 2310 900 899 935 36 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 899 NA -36 phiX1 + 2310 1155 1154 1190 36 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1154 NA +36 phiX1 + 2310 962 961 997 36 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 961 NA 36 phiX1 + 2310 989 988 1024 36 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGAGGATAAATTATGTCTAATATTCAAACTGGCGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 988 NA -36 phiX1 + 2310 1207 1206 1242 36 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTTTATGTCCCTCATCGTCACGTTTATGGTGAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1206 NA -36 phiX1 + 2310 2116 2115 2151 36 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2115 NA -36 phiX1 + 2310 660 659 695 36 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 659 NA -31 phiX1 + 2310 1807 1806 1837 31 TAAACATTCTGTGCCGCGTTTCTTTGTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TAAACATTCTGTGCCGCGTTTCTTTGTTCCT ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1806 NA -36 phiX1 + 2310 1536 1535 1571 36 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGCTTTCTCGCCAAATGACGACTTCTACCACATCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1535 NA -35 phiX1 + 2310 2112 2111 2146 35 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2110 NA -36 phiX1 + 2310 1948 1947 1983 36 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1947 NA -35 phiX1 + 2310 2212 2211 2246 35 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAGTCAGGTTAAATTTAATGTGACCGTTTATCGCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2211 NA -16 phiX1 + 2310 424 423 447 24 AGACCGCTTTGGCCTCTATTAAGC HWI-EAS91_1_306UPAAXX - 36 3 2 26 11 10 34 24 AGACCGCCTTGGCCTCTATTAAGC .......:................ 24M 23/24 95.8% 24/36 66.7% 0/24 0.0% 421 NA -35 phiX1 + 2310 1940 1939 1974 35 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1938 NA -35 phiX1 + 2310 1274 1273 1308 35 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCCACTCCTCTCCCGACTGTTAACACTACTGGTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1272 NA -36 phiX1 + 2310 1707 1706 1742 36 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1706 NA -36 phiX1 + 2310 1582 1581 1617 36 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1581 NA -36 phiX1 + 2310 1588 1587 1623 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCAAGCTGCTTATGCTAATTTGCATACTGACCAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1587 NA -34 phiX1 + 2310 1180 1179 1213 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1179 NA -22 phiX1 + 2310 2289 2288 2310 22 AGATTGAGTGTGAGGTTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 22 15 14 36 22 AGATTGAGTGTGAGGTTATAAC ...................... 22M 22/22 100.0% 22/36 61.1% 0/22 0.0% 2288 22 -36 phiX1 + 2310 441 440 476 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 440 NA -36 phiX1 + 2310 1012 1011 1047 36 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1011 NA -36 phiX1 + 2310 161 160 196 36 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 160 NA -35 phiX1 + 2310 1165 1164 1199 35 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCGTCGTGGCCTTGCTATTGACTCTACTGTAGACA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1163 NA -25 phiX1 + 2310 2286 2285 2310 25 AAAAGATTGAGTGTGAGGTTATAAC HWI-EAS91_1_306UPAAXX - 36 1 0 25 12 11 36 25 AAAAGATTGAGTGTGAGGTTATAAC ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 2285 25 -32 phiX1 + 2310 801 800 832 32 GCAGAAGAAAACGTGCGTCAAAAATTACGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 32 5 4 36 32 GCAGAAGAAAACGTGCGTCAAAAATTACGTGC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 800 NA -36 phiX1 + 2310 1587 1586 1622 36 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCAAGCTGCTTATGCTAATTTGCATACTGACCAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1586 NA -36 phiX1 + 2310 496 495 531 36 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCTGACGAGTAACAAAGTTTGGATTGCTACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 495 NA -36 phiX1 + 2310 441 440 476 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 440 NA -35 phiX1 + 2310 1579 1578 1613 35 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1577 NA -18 phiX1 + 2310 657 656 674 18 AACATTCAAACGGCCTGT HWI-EAS91_1_306UPAAXX - 36 19 18 36 1 0 18 18 AACATTCAAACGGCCTGT .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 638 NA -32 phiX1 + 2310 1 0 32 32 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA HWI-EAS91_1_306UPAAXX - 36 5 4 36 1 0 32 32 GAGTTTTATCGCTTCCATGACGCAGAAGTTAA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% -4 -32 -36 phiX1 + 2310 54 53 89 36 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTCGAAAAATTATCTTGATAAAGCAGGAATTACTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 53 NA -35 phiX1 + 2310 680 679 714 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 678 NA -36 phiX1 + 2310 231 230 266 36 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 230 NA -36 phiX1 + 2310 1580 1579 1615 36 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1579 NA -36 phiX1 + 2310 611 610 646 36 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 610 NA -30 phiX1 + 2310 638 637 667 30 TTATTATGTTCATCCCGTCAACATTCAAAC HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TTATTATGTTCATCCCGTCAACATTCAAAC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 637 NA -36 phiX1 + 2310 1957 1956 1992 36 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1956 NA -35 phiX1 + 2310 540 539 574 35 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 538 NA -36 phiX1 + 2310 1852 1851 1887 36 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1851 NA -36 phiX1 + 2310 584 583 619 36 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 583 NA -36 phiX1 + 2310 1728 1727 1763 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCTGGGCATCTGGCTATGATGTTGATGGAACTGACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1727 NA -36 phiX1 + 2310 1721 1720 1756 36 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1720 NA -36 phiX1 + 2310 1954 1953 1989 36 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1953 NA -36 phiX1 + 2310 962 961 997 36 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 961 NA -36 phiX1 + 2310 2175 2174 2210 36 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2174 NA -36 phiX1 + 2310 2004 2003 2039 36 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2003 NA -36 phiX1 + 2310 2154 2153 2189 36 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATTCGCCACCATGATTATGACCAGTGTTTCCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2153 NA -35 phiX1 + 2310 1093 1092 1127 35 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTCAACTACTCCGGTTATCGCTGGCGACTCCTTCG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1092 NA -36 phiX1 + 2310 1734 1733 1769 36 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATCTGGCTATGATGTTGATGGAACTGACCAAACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1733 NA -36 phiX1 + 2310 1522 1521 1557 36 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1521 NA -36 phiX1 + 2310 409 408 444 36 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 AATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 408 NA -36 phiX1 + 2310 1867 1866 1902 36 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1866 NA -36 phiX1 + 2310 1242 1241 1277 36 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1241 NA -35 phiX1 + 2310 527 526 561 35 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 526 NA -36 phiX1 + 2310 2100 2099 2135 36 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 AAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2099 NA -36 phiX1 + 2310 1002 1001 1037 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1001 NA -35 phiX1 + 2310 10 9 44 35 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CGCTTCCATGACGCAGAAGTTAACACTTTCGGATA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 8 NA -36 phiX1 + 2310 1579 1578 1614 36 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGGGTCTGCAAGCTGCTTATGCTAATTTGCATAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1578 NA -30 phiX1 + 2310 989 988 1018 30 TGAGGATAAATTATGTCTAATATTCAAACT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TGAGGATAAATTATGTCTAATATTCAAACT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 988 NA -36 phiX1 + 2310 349 348 384 36 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 348 NA -36 phiX1 + 2310 286 285 321 36 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 285 NA -35 phiX1 + 2310 680 679 714 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATGGAAGGCGCTGAATTTACGGAAAACATTATTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 678 NA -34 phiX1 + 2310 320 319 353 34 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TTGACATTTTAAAAGAGCGTGGATTACTATCTGA .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 319 NA -34 phiX1 + 2310 1180 1179 1213 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 TATTGACTCTACTGTAGACATTTTTACTTTTTAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1179 NA -36 phiX1 + 2310 521 520 556 36 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 520 NA -36 phiX1 + 2310 333 332 368 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 332 NA -36 phiX1 + 2310 72 71 107 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATAAAGCAGGAATTACTACTGCTTGTTTACGAATTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 71 NA -36 phiX1 + 2310 1974 1973 2009 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1973 NA -35 phiX2 + 3076 1985 1984 2019 35 CCCCCAACTTGATATTAATAACACTATAGACCACC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCCCCAACTTGATATTAATAACACTATAGACCACC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1983 NA +36 phiX2 + 3076 1001 1000 1036 36 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1000 NA +36 phiX2 + 3076 1003 1002 1038 36 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1002 NA +36 phiX2 + 3076 1016 1015 1051 36 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1015 NA +36 phiX2 + 3076 1034 1033 1069 36 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1033 NA +36 phiX2 + 3076 1058 1057 1093 36 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1057 NA +36 phiX2 + 3076 1085 1084 1120 36 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1084 NA +36 phiX2 + 3076 1098 1097 1133 36 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1097 NA +36 phiX2 + 3076 1110 1109 1145 36 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1109 NA +36 phiX2 + 3076 1149 1148 1184 36 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1148 NA +36 phiX2 + 3076 1154 1153 1189 36 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1153 NA +36 phiX2 + 3076 1162 1161 1197 36 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1161 NA +36 phiX2 + 3076 1194 1193 1229 36 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1193 NA +36 phiX2 + 3076 1210 1209 1245 36 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1209 NA 36 phiX2 + 3076 1212 1211 1247 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1211 NA -33 phiX2 + 3076 2253 2252 2285 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGTTGGTTTATCGTTTTTGACACTCTCACGTTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 2252 NA +36 phiX2 + 3076 1230 1229 1265 36 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1229 NA +36 phiX2 + 3076 1234 1233 1269 36 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1233 NA +36 phiX2 + 3076 1253 1252 1288 36 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1252 NA +36 phiX2 + 3076 126 125 161 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 125 NA +36 phiX2 + 3076 126 125 161 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 125 NA +36 phiX2 + 3076 1260 1259 1295 36 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1259 NA +36 phiX2 + 3076 1262 1261 1297 36 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1261 NA +36 phiX2 + 3076 1263 1262 1298 36 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1262 NA +36 phiX2 + 3076 1277 1276 1312 36 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1276 NA +36 phiX2 + 3076 1282 1281 1317 36 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1281 NA +36 phiX2 + 3076 1290 1289 1325 36 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1289 NA +36 phiX2 + 3076 1307 1306 1342 36 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1306 NA +36 phiX2 + 3076 1309 1308 1344 36 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1308 NA +36 phiX2 + 3076 1316 1315 1351 36 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1315 NA +36 phiX2 + 3076 1319 1318 1354 36 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1318 NA +36 phiX2 + 3076 132 131 167 36 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 131 NA +36 phiX2 + 3076 1364 1363 1399 36 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1363 NA +36 phiX2 + 3076 1389 1388 1424 36 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1388 NA +36 phiX2 + 3076 1398 1397 1433 36 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1397 NA +36 phiX2 + 3076 1402 1401 1437 36 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1401 NA +36 phiX2 + 3076 1421 1420 1456 36 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1420 NA +36 phiX2 + 3076 143 142 178 36 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 142 NA +36 phiX2 + 3076 1446 1445 1481 36 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1445 NA +36 phiX2 + 3076 1451 1450 1486 36 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1450 NA +36 phiX2 + 3076 1477 1476 1512 36 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1476 NA +36 phiX2 + 3076 1539 1538 1574 36 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1538 NA +36 phiX2 + 3076 1548 1547 1583 36 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1547 NA +36 phiX2 + 3076 1551 1550 1586 36 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1550 NA +36 phiX2 + 3076 1552 1551 1587 36 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1551 NA +36 phiX2 + 3076 1553 1552 1588 36 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1552 NA +36 phiX2 + 3076 1610 1609 1645 36 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1609 NA +36 phiX2 + 3076 1668 1667 1703 36 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1667 NA +36 phiX2 + 3076 1669 1668 1704 36 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1668 NA +36 phiX2 + 3076 1672 1671 1707 36 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1671 NA +36 phiX2 + 3076 1678 1677 1713 36 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1677 NA +36 phiX2 + 3076 169 168 204 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 168 NA +36 phiX2 + 3076 169 168 204 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 168 NA +36 phiX2 + 3076 1690 1689 1725 36 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1689 NA +36 phiX2 + 3076 1695 1694 1730 36 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1694 NA +36 phiX2 + 3076 1716 1715 1751 36 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1715 NA +36 phiX2 + 3076 1729 1728 1764 36 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1728 NA +36 phiX2 + 3076 1733 1732 1768 36 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1732 NA +36 phiX2 + 3076 1753 1752 1788 36 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1752 NA +36 phiX2 + 3076 1785 1784 1820 36 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1784 NA +36 phiX2 + 3076 1788 1787 1823 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1787 NA +36 phiX2 + 3076 1789 1788 1824 36 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1788 NA +36 phiX2 + 3076 1816 1815 1851 36 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1815 NA +36 phiX2 + 3076 1820 1819 1855 36 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1819 NA +36 phiX2 + 3076 1822 1821 1857 36 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1821 NA +36 phiX2 + 3076 1860 1859 1895 36 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1859 NA +36 phiX2 + 3076 1864 1863 1899 36 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1863 NA +36 phiX2 + 3076 1866 1865 1901 36 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1865 NA +36 phiX2 + 3076 1882 1881 1917 36 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1881 NA +36 phiX2 + 3076 1886 1885 1921 36 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1885 NA +36 phiX2 + 3076 1893 1892 1928 36 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1892 NA +36 phiX2 + 3076 1907 1906 1942 36 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1906 NA +36 phiX2 + 3076 1938 1937 1973 36 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1937 NA +36 phiX2 + 3076 1939 1938 1974 36 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1938 NA +36 phiX2 + 3076 1944 1943 1979 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1943 NA +36 phiX2 + 3076 1944 1943 1979 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1943 NA +36 phiX2 + 3076 1946 1945 1981 36 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1945 NA +36 phiX2 + 3076 1950 1949 1985 36 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1949 NA +36 phiX2 + 3076 1972 1971 2007 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1971 NA +36 phiX2 + 3076 1972 1971 2007 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1971 NA +36 phiX2 + 3076 2071 2070 2106 36 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA +36 phiX2 + 3076 2094 2093 2129 36 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2093 NA +36 phiX2 + 3076 2104 2103 2139 36 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2103 NA +36 phiX2 + 3076 2118 2117 2153 36 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2117 NA +36 phiX2 + 3076 2124 2123 2159 36 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2123 NA +36 phiX2 + 3076 2130 2129 2165 36 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2129 NA +36 phiX2 + 3076 2161 2160 2196 36 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2160 NA +36 phiX2 + 3076 2229 2228 2264 36 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2228 NA +36 phiX2 + 3076 2241 2240 2276 36 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2240 NA +36 phiX2 + 3076 2250 2249 2285 36 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2249 NA +36 phiX2 + 3076 2268 2267 2303 36 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2267 NA +36 phiX2 + 3076 2286 2285 2321 36 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2285 NA +36 phiX2 + 3076 2296 2295 2331 36 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2295 NA +36 phiX2 + 3076 2298 2297 2333 36 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2297 NA +36 phiX2 + 3076 2374 2373 2409 36 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2373 NA +36 phiX2 + 3076 2380 2379 2415 36 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2379 NA +36 phiX2 + 3076 2430 2429 2465 36 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2429 NA +36 phiX2 + 3076 247 246 282 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 246 NA +36 phiX2 + 3076 247 246 282 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 246 NA +36 phiX2 + 3076 2478 2477 2513 36 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2477 NA +36 phiX2 + 3076 2482 2481 2517 36 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2481 NA +36 phiX2 + 3076 2530 2529 2565 36 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2529 NA +36 phiX2 + 3076 2555 2554 2590 36 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2554 NA +36 phiX2 + 3076 2556 2555 2591 36 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2555 NA +36 phiX2 + 3076 2574 2573 2609 36 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2573 NA +36 phiX2 + 3076 2581 2580 2616 36 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2580 NA +36 phiX2 + 3076 2599 2598 2634 36 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2598 NA +36 phiX2 + 3076 2626 2625 2661 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2625 NA +36 phiX2 + 3076 2626 2625 2661 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2625 NA +36 phiX2 + 3076 2627 2626 2662 36 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2626 NA +36 phiX2 + 3076 2635 2634 2670 36 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2634 NA +36 phiX2 + 3076 264 263 299 36 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 263 NA +36 phiX2 + 3076 2640 2639 2675 36 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2639 NA +36 phiX2 + 3076 2645 2644 2680 36 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2644 NA +36 phiX2 + 3076 2647 2646 2682 36 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2646 NA +36 phiX2 + 3076 267 266 302 36 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 266 NA +36 phiX2 + 3076 2671 2670 2706 36 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2670 NA +36 phiX2 + 3076 2695 2694 2730 36 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2694 NA +36 phiX2 + 3076 2723 2722 2758 36 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2722 NA +36 phiX2 + 3076 2729 2728 2764 36 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2728 NA +36 phiX2 + 3076 2742 2741 2777 36 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2741 NA +36 phiX2 + 3076 2763 2762 2798 36 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2762 NA +36 phiX2 + 3076 2767 2766 2802 36 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2766 NA +36 phiX2 + 3076 2789 2788 2824 36 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2788 NA +36 phiX2 + 3076 2795 2794 2830 36 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2794 NA +36 phiX2 + 3076 2797 2796 2832 36 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2796 NA +36 phiX2 + 3076 282 281 317 36 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 281 NA +36 phiX2 + 3076 2841 2840 2876 36 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2840 NA +36 phiX2 + 3076 2842 2841 2877 36 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2841 NA +36 phiX2 + 3076 2847 2846 2882 36 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2846 NA +36 phiX2 + 3076 2852 2851 2887 36 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2851 NA +36 phiX2 + 3076 2866 2865 2901 36 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2865 NA +36 phiX2 + 3076 2869 2868 2904 36 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2868 NA +36 phiX2 + 3076 2877 2876 2912 36 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2876 NA +36 phiX2 + 3076 2896 2895 2931 36 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2895 NA +36 phiX2 + 3076 2962 2961 2997 36 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2961 NA +36 phiX2 + 3076 311 310 346 36 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 310 NA 36 phiX2 + 3076 358 357 393 36 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 357 NA -36 phiX2 + 3076 1938 1937 1973 36 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTACTGAGAAGTTAATGGATGAATTGGCACAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1937 NA -36 phiX2 + 3076 553 552 588 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 552 NA -36 phiX2 + 3076 247 246 282 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 246 NA -34 phiX2 + 3076 201 200 234 34 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GTCAACGTTATATTTTGATAGTTTGACGGTTAAT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 200 NA -36 phiX2 + 3076 2842 2841 2877 36 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATGAAAATGCTCACAATGACAAATCTGTCCACGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2841 NA -36 phiX2 + 3076 2574 2573 2609 36 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTACAGTATGCCCATCGCAGTTCGCTACACGCAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2573 NA -36 phiX2 + 3076 2742 2741 2777 36 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2741 NA -36 phiX2 + 3076 2599 2598 2634 36 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2598 NA -36 phiX2 + 3076 553 552 588 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 552 NA -30 phiX2 + 3076 1863 1862 1892 30 GTTGAGTTCGATAATGGTGATATGTATGTT HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GTTGAGTTCGATAATGGTGATATGTATGTT .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1862 NA -35 phiX2 + 3076 816 815 850 35 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 814 NA -36 phiX2 + 3076 903 902 938 36 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 902 NA -36 phiX2 + 3076 1110 1109 1145 36 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1109 NA -33 phiX2 + 3076 572 571 604 33 AGGTTATTAAAGAGATTATTTGTCTCCAGCCAC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 AGGTTATTAAAGAGATTATTTGTCTCCAGCCAC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 568 NA -36 phiX2 + 3076 2161 2160 2196 36 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2160 NA -36 phiX2 + 3076 71 70 106 36 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 70 NA -36 phiX2 + 3076 1788 1787 1823 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1787 NA -36 phiX2 + 3076 2789 2788 2824 36 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2788 NA -36 phiX2 + 3076 1944 1943 1979 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1943 NA -36 phiX2 + 3076 1098 1097 1133 36 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACAATCAGAAAGAGATTGCCGAGATGCAAAATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1097 NA -36 phiX2 + 3076 1733 1732 1768 36 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1732 NA -36 phiX2 + 3076 2250 2249 2285 36 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGGTTGGTTTATCGTTTTTGACACTCTCACGTTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2249 NA -35 phiX2 + 3076 1124 1123 1158 35 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCAAAATGAGACTCAAAAAGAGATTGCTGGCATTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1122 NA -36 phiX2 + 3076 2229 2228 2264 36 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAATGCGACAGGCTCATGCTGATGGTTGGTTTATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2228 NA -36 phiX2 + 3076 1398 1397 1433 36 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTTAGTTCATCAGCAAACGCAGAATCAGCGGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1397 NA -36 phiX2 + 3076 1016 1015 1051 36 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1015 NA -36 phiX2 + 3076 1866 1865 1901 36 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTTCGATAATGGTGATATGTATGTTGACGGCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1865 NA -36 phiX2 + 3076 247 246 282 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGTTTTCTTCATTGCATTCAGATGGATACATCTGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 246 NA -36 phiX2 + 3076 967 966 1002 36 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 966 NA -36 phiX2 + 3076 1282 1281 1317 36 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1281 NA -36 phiX2 + 3076 1194 1193 1229 36 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATATGCACAAAATGAGATGCTTGCTTATCAACAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1193 NA -36 phiX2 + 3076 1316 1315 1351 36 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1315 NA -36 phiX2 + 3076 1262 1261 1297 36 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1261 NA -36 phiX2 + 3076 1944 1943 1979 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGAAGTTAATGGATGAATTGGCACAATGCTACAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1943 NA -36 phiX2 + 3076 1860 1859 1895 36 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGCGTTGAGTTCGATAATGGTGATATGTATGTTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1859 NA -30 phiX2 + 3076 502 501 531 30 GTTTATGTTGGTTTCATGGTTTGGTCTAAC HWI-EAS91_1_306UPAAXX - 36 7 6 36 1 0 30 30 GTTTATGTTGGTTTCATGGTTTGGTCTAAC .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 495 NA -36 phiX2 + 3076 809 808 844 36 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 808 NA -35 phiX2 + 3076 440 439 474 35 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTTATTATACCGTCAAGGACTGTGTGACTATTGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 439 NA -36 phiX2 + 3076 2296 2295 2331 36 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GATTAGAGGCGTTTTATGATAATCCCAATGCTTTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2295 NA -36 phiX2 + 3076 1263 1262 1298 36 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1262 NA -36 phiX2 + 3076 2795 2794 2830 36 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2794 NA -36 phiX2 + 3076 1785 1784 1820 36 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1784 NA -36 phiX2 + 3076 2241 2240 2276 36 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2240 NA -36 phiX2 + 3076 974 973 1009 36 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 973 NA -20 phiX2 + 3076 628 627 647 20 GTGCTATTGCTGGCGGTATT HWI-EAS91_1_306UPAAXX + 36 1 0 20 1 0 20 20 GTGCTATTGCTGGCGGTATT .................... 20M 20/20 100.0% 20/36 55.6% 0/20 0.0% 627 NA -36 phiX2 + 3076 1695 1694 1730 36 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAATGTCACGCTGATTATTTTGACTTTGAGCGTATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1694 NA -36 phiX2 + 3076 169 168 204 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 168 NA -35 phiX2 + 3076 735 734 769 35 GCTACCGATAACAATACTGTAGGCATGGGTGATGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GCTACCGATAACAATACTGTAGGCATGGGTGATGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 733 NA -36 phiX2 + 3076 2962 2961 2997 36 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2961 NA -30 phiX2 + 3076 2020 2019 2055 36 GCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCCCGAAGGGGACNANAAATGGTTTTTAGAGAACG ..............X.X................... 36M 34/34 100.0% 36/36 100.0% 0/36 0.0% 2019 NA -36 phiX2 + 3076 2581 2580 2616 36 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2580 NA -34 phiX2 + 3076 2475 2474 2508 34 TTTATGCGGACACTTCCTACAGGTAGCGTTGACC HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 TTTATGCGGACACTTCCTACAGGTAGCGTTGACC .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2472 NA -36 phiX2 + 3076 1309 1308 1344 36 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1308 NA -32 phiX2 + 3076 2145 2144 2176 32 GGTATTAAGGATGAGTGTTCAAGATTGCTGGA HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 GGTATTAAGGATGAGTGTTCAAGATTGCTGGA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 2144 NA -35 phiX2 + 3076 654 653 688 35 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 653 NA +36 phiX2 + 3076 379 378 414 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA +36 phiX2 + 3076 379 378 414 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA +36 phiX2 + 3076 388 387 423 36 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 387 NA +36 phiX2 + 3076 400 399 435 36 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 399 NA +36 phiX2 + 3076 418 417 453 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 417 NA +36 phiX2 + 3076 418 417 453 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 417 NA +36 phiX2 + 3076 428 427 463 36 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 427 NA +36 phiX2 + 3076 439 438 474 36 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 438 NA +36 phiX2 + 3076 444 443 479 36 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 443 NA +36 phiX2 + 3076 446 445 481 36 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 445 NA +36 phiX2 + 3076 452 451 487 36 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 451 NA 36 phiX2 + 3076 453 452 488 36 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 452 NA 36 phiX2 + 3076 456 455 491 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 455 NA +36 phiX2 + 3076 456 455 491 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 455 NA +36 phiX2 + 3076 465 464 500 36 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 464 NA +36 phiX2 + 3076 505 504 540 36 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 504 NA +36 phiX2 + 3076 506 505 541 36 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 505 NA +36 phiX2 + 3076 540 539 575 36 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 539 NA +36 phiX2 + 3076 553 552 588 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 552 NA +36 phiX2 + 3076 553 552 588 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 552 NA +36 phiX2 + 3076 563 562 598 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 562 NA +36 phiX2 + 3076 563 562 598 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 562 NA +36 phiX2 + 3076 569 568 604 36 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 568 NA +36 phiX2 + 3076 624 623 659 36 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 623 NA +36 phiX2 + 3076 633 632 668 36 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 632 NA +36 phiX2 + 3076 691 690 726 36 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 690 NA +36 phiX2 + 3076 705 704 740 36 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 704 NA +36 phiX2 + 3076 71 70 106 36 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 70 NA +36 phiX2 + 3076 711 710 746 36 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 710 NA +36 phiX2 + 3076 772 771 807 36 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 771 NA +36 phiX2 + 3076 783 782 818 36 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 782 NA +36 phiX2 + 3076 786 785 821 36 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 785 NA 36 phiX2 + 3076 790 789 825 36 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 789 NA -36 phiX2 + 3076 1816 1815 1851 36 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1815 NA -36 phiX2 + 3076 1716 1715 1751 36 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1715 NA -36 phiX2 + 3076 311 310 346 36 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGCTGATATTGCTTTTGATGCCGACCCTAAATTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 310 NA -36 phiX2 + 3076 439 438 474 36 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTTATTATACCGTCAAGGACTGTGTGACTATTGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 438 NA -36 phiX2 + 3076 563 562 598 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 562 NA -36 phiX2 + 3076 1553 1552 1588 36 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1552 NA -36 phiX2 + 3076 2877 2876 2912 36 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAGTGCTTAATCCAACTTACCAAGCTGGGTTACGAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2876 NA -36 phiX2 + 3076 1886 1885 1921 36 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1885 NA -36 phiX2 + 3076 2847 2846 2882 36 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAAATGCTCACAATGACAAATCTGTCCACGGAGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2846 NA -36 phiX2 + 3076 2530 2529 2565 36 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2529 NA -29 phiX2 + 3076 953 952 981 29 TGATAAAGGAAAGGATACTCGTGATTATC HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 TGATAAAGGAAAGGATACTCGTGATTATC ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 945 NA -28 phiX2 + 3076 171 170 206 36 ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC ..........x......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 170 NA -36 phiX2 + 3076 1668 1667 1703 36 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTATGGTTCGTTCTTATTACCCTTCTGAATGTCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1667 NA -36 phiX2 + 3076 2555 2554 2590 36 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2554 NA +36 phiX2 + 3076 809 808 844 36 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 808 NA +36 phiX2 + 3076 817 816 852 36 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 816 NA +36 phiX2 + 3076 841 840 876 36 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 840 NA +36 phiX2 + 3076 857 856 892 36 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 856 NA +36 phiX2 + 3076 903 902 938 36 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 902 NA +36 phiX2 + 3076 940 939 975 36 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 939 NA +36 phiX2 + 3076 951 950 986 36 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 950 NA 36 phiX2 + 3076 961 960 996 36 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 960 NA -36 phiX2 + 3076 1864 1863 1899 36 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAGTTCGATAATGGTGATATGTATGTTGACGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1863 NA -30 phiX2 + 3076 1500 1499 1529 30 GTGGTTGATATTTTTCATGGTATTGATAAA HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GTGGTTGATATTTTTCATGGTATTGATAAA .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1499 NA -28 phiX2 + 3076 2325 2324 2352 28 GCTTTGCGTGACTATTTTCGTGATATTG HWI-EAS91_1_306UPAAXX + 36 1 0 28 1 0 28 28 GCTTTGCGTGACTATTTTCGTGATATTG ............................ 28M 28/28 100.0% 28/36 77.8% 0/28 0.0% 2324 NA -36 phiX2 + 3076 428 427 463 36 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCATGATGGTGGTTATTATACCGTCAAGGACTGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 427 NA -35 phiX2 + 3076 393 392 427 35 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCCGACTGCCTATGATGTTTATCCTTTGAATGGTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 391 NA -36 phiX2 + 3076 633 632 668 36 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 632 NA -36 phiX2 + 3076 1551 1550 1586 36 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1550 NA -36 phiX2 + 3076 783 782 818 36 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 782 NA -36 phiX2 + 3076 841 840 876 36 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 840 NA -36 phiX2 + 3076 2482 2481 2517 36 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGACACTTCCTACAGGTAGCGTTGACCCTAATTTTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2481 NA -36 phiX2 + 3076 1539 1538 1574 36 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATACTTGGAACAATTTCTGGAAAGACGGTAAAGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1538 NA -35 phiX2 + 3076 433 432 467 35 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GATGGTGGTTATTATACCGTCAAGGACTGTGTGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 431 NA -36 phiX2 + 3076 705 704 740 36 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 704 NA -36 phiX2 + 3076 2556 2555 2591 36 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAAATACGTGGCCTTATGGTTACAGTATGCCCATC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2555 NA -36 phiX2 + 3076 2094 2093 2129 36 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GAACGCCCTCTTAAGGATATTCGCGATGAGTATAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2093 NA -36 phiX2 + 3076 2852 2851 2887 36 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTCACAATGACAAATCTGTCCACGGAGTGCTTAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2851 NA -36 phiX2 + 3076 951 950 986 36 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGATAAAGGAAAGGATACTCGTGATTATCTTGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 950 NA -36 phiX2 + 3076 786 785 821 36 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 785 NA -35 phiX2 + 3076 502 501 536 35 GTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GTTTATGTTGGTTTCATGGTTTGGTCTAACTTTAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 500 NA -36 phiX2 + 3076 1149 1148 1184 36 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGGCATTCAGTCGGCGACTTCACGCCAGAATACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1148 NA -36 phiX2 + 3076 1389 1388 1424 36 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1388 NA -31 phiX2 + 3076 331 330 361 31 GCCGACCCTAAATTTTTTGCCTGTTTGGTTC HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GCCGACCCTAAATTTTTTGCCTGTTTGGTTC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 330 NA -35 phiX2 + 3076 756 755 790 35 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GGCATGGGTGATGCTGGTATTAAATCTGCCATTCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 755 NA -36 phiX2 + 3076 2118 2117 2153 36 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGAGTATAATTACCCCAAAAAGAAAGGTATTAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2117 NA -36 phiX2 + 3076 1690 1689 1725 36 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTTCTGAATGTCACGCTGATTATTTTGACTTTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1689 NA -33 phiX2 + 3076 884 883 916 33 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCAGGCTGGCACTTCTGCCGTTTCTGATAAGTT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 883 NA -36 phiX2 + 3076 2286 2285 2321 36 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTGACGACCGATTAGAGGCGTTTTATGATAATCCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2285 NA -36 phiX2 + 3076 563 562 598 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 562 NA -36 phiX2 + 3076 379 378 414 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA -35 phiX2 + 3076 2881 2880 2915 35 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GCTTAATCCAACTTACCAAGCTGGGTTACGACGCG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2880 NA -18 phiX2 + 3076 1421 1420 1438 18 GAATCAGCGGTATGGCTC HWI-EAS91_1_306UPAAXX + 36 1 0 18 1 0 18 18 GAATCAGCGGTATGGCTC .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 1420 NA -28 phiX2 + 3076 660 659 695 36 GCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTGGTGGCGCCATGTCTAAATTTTTTGGAGGCGGT .......................x............ 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 659 NA -36 phiX2 + 3076 2841 2840 2876 36 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGGATGAAAATGCTCACAATGACAAATCTGTCCACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2840 NA -35 phiX2 + 3076 2578 2577 2612 35 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACAGTATGCCCATCGCAGTTCGCTACACGCAGGAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2576 NA -33 phiX2 + 3076 1662 1661 1694 33 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GGCTTTTTTATGGTTCGTTCTTATTACCCTTCT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1661 NA -36 phiX2 + 3076 2723 2722 2758 36 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2722 NA -36 phiX2 + 3076 2640 2639 2675 36 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2639 NA -34 phiX2 + 3076 2174 2173 2207 34 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTT HWI-EAS91_1_306UPAAXX - 36 1 0 34 3 2 36 34 GGAGGCCTCCACTATGAAATCGCGTAGAGGCTTT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2173 NA -27 phiX2 + 3076 2457 2456 2491 35 CATTTCCATGCGGTGCACTTTATGCGGACACTTCC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CATTTCCATGCGGTGCATTTTATGCGGACACTTCC .................:................. 35M 34/35 97.1% 35/36 97.2% 0/35 0.0% 2455 NA -36 phiX2 + 3076 267 266 302 36 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GATGGATACATCTGTCAACGCCGCTAATCAGGTTGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 266 NA -36 phiX2 + 3076 711 710 746 36 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 710 NA -36 phiX2 + 3076 1421 1420 1456 36 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAATCAGCGGTATGGCTCTTCTCATATTGGCGCTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1420 NA -36 phiX2 + 3076 126 125 161 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 125 NA -36 phiX2 + 3076 400 399 435 36 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCCTATGATGTTTATCCTTTGAATGGTCGCCATGAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 399 NA -28 phiX2 + 3076 1918 1917 1945 28 TTCGTGATGAGTTTGTATCTGTTACTGA HWI-EAS91_1_306UPAAXX + 36 1 0 28 1 0 28 28 TTCGTGATGAGTTTGTATCTGTTACTGA ............................ 28M 28/28 100.0% 28/36 77.8% 0/28 0.0% 1917 NA -34 phiX2 + 3076 2296 2295 2329 34 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GATTAGAGGCGTTTTATGATAATCCCAATGCTTT .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2295 NA -36 phiX2 + 3076 456 455 491 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GGACTGTGTGACTATTGACGTCCTTCCCCGTACGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 455 NA -26 phiX2 + 3076 1726 1725 1751 26 GTATCGAGGCTCTTAAACCTGCTATT HWI-EAS91_1_306UPAAXX + 36 1 0 26 1 0 26 26 GTATCGAGGCTCTTAAACCTGCTATT .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 1725 NA -36 phiX2 + 3076 940 939 975 36 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 939 NA -29 phiX2 + 3076 1176 1175 1204 29 CAGAATACGAAAGACCAGGTATATGCACA HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 CAGAATACGAAAGACCAGGTATATGCACA ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 1168 NA -21 phiX2 + 3076 942 941 970 29 AAGTCTGCCGCTGATAAAGGAAAGGATAC HWI-EAS91_1_306UPAAXX - 36 8 7 36 1 0 29 29 AAGTCTGCCGATGATAAAGGAAAGGATAC ..........x.................. 29M 28/29 96.6% 29/36 80.6% 0/29 0.0% 934 NA -36 phiX2 + 3076 1972 1971 2007 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1971 NA -34 phiX2 + 3076 1826 1825 1859 34 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 34 1 0 34 34 GCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAG .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 1825 NA -36 phiX2 + 3076 2104 2103 2139 36 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAAGGATATTCGCGATGAGTATAATTACCCCAAAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2103 NA -36 phiX2 + 3076 1678 1677 1713 36 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTTCTTATTACCCTTCTGAATGTCACGCTGATTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1677 NA -36 phiX2 + 3076 1893 1892 1928 36 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1892 NA -28 phiX2 + 3076 1788 1787 1823 36 ATGCTTGGCTTCCATAAGCAGATGGATAACCGCATC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTTGGCTTCAATAAGCAGATGGATAACCGCATC ............x....................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 1787 NA -35 phiX2 + 3076 1997 1996 2031 35 TATTAATAACACTATAGACCACCGCCCCGAAGGGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATTAATAACACTATAGACCACCGCCCCGAAGGGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1996 NA -36 phiX2 + 3076 379 378 414 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTTCCGACTACCCTCCCGACTGCCTATGATGTTTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 378 NA -33 phiX2 + 3076 2606 2605 2638 33 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCAGGACGCTTTTTCACGTTCTGGTTGGTTGTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 2605 NA -29 phiX2 + 3076 1518 1517 1546 29 GGTATTGATAAAGCTGTTGCCGATACTTG HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GGTATTGATAAAGCTGTTGCCGATACTTG ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 1517 NA -36 phiX2 + 3076 1446 1445 1481 36 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1445 NA -28 phiX2 + 3076 789 788 824 36 CAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAGGCTCTAATGTTCCTAACCCTGATGGGGCCGCC ............................:....... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 788 NA -36 phiX2 + 3076 772 771 807 36 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 771 NA -27 phiX2 + 3076 1911 1910 1937 27 TCTGACGTTCGTGATGAGTTTGTATCT HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 TCTGACGTTCGTGATGAGTTTGTATCT ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 1910 NA -36 phiX2 + 3076 2626 2625 2661 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2625 NA -36 phiX2 + 3076 2380 2379 2415 36 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCAAGGCTAATGATTCACACGCCGACTGCTATCAGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2379 NA -23 phiX2 + 3076 237 236 267 31 TGGTAATGGTGGTTTTCTTCATTGCATTCAG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TGGTAATGGTGGTTTTCTTCATTTCATTCAG .......................x....... 31M 30/31 96.8% 31/36 86.1% 0/31 0.0% 236 NA -36 phiX2 + 3076 1210 1209 1245 36 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1209 NA -36 phiX2 + 3076 1548 1547 1583 36 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AACAATTTCTGGAAAGACGGTAAAGCTGATGGTATT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1547 NA -36 phiX2 + 3076 1034 1033 1069 36 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1033 NA -27 phiX2 + 3076 2362 2361 2388 27 TTCTTGCTGCCGAGGGTCGCAAGGCTA HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 TTCTTGCTGCCGAGGGTCGCAAGGCTA ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 2361 NA -36 phiX2 + 3076 2767 2766 2802 36 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GGAACAACTCACTAAAAACCAAGCTGTCGCTACTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2766 NA -35 phiX2 + 3076 453 452 487 35 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 451 NA -36 phiX2 + 3076 1972 1971 2007 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTACAATGTGCTCCCCCAACTTGATATTAATAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1971 NA -27 phiX2 + 3076 2346 2345 2372 27 GATATTGGTCGTATGGTTCTTGCTGCC HWI-EAS91_1_306UPAAXX + 36 1 0 27 1 0 27 27 GATATTGGTCGTATGGTTCTTGCTGCC ........................... 27M 27/27 100.0% 27/36 75.0% 0/27 0.0% 2345 NA -18 phiX2 + 3076 2625 2624 2642 18 TCTGGTTGGTTGTGGCCT HWI-EAS91_1_306UPAAXX + 36 1 0 18 1 0 18 18 TCTGGTTGGTTGTGGCCT .................. 18M 18/18 100.0% 18/36 50.0% 0/18 0.0% 2624 NA -36 phiX2 + 3076 2797 2796 2832 36 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2796 NA -35 phiX2 + 3076 2858 2857 2892 35 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 AATGACAAATCTGTCCACGGAGTGCTTAATCCAAC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2856 NA -28 phiX2 + 3076 646 645 681 36 TTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTGCTTCTGCTCTTGCTTGTGGCGCCATGTCTAAAT .................x.................. 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 645 NA -36 phiX2 + 3076 1319 1318 1354 36 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1318 NA -36 phiX2 + 3076 169 168 204 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCACCTGTTTTACAGACACCTAAAGCTACATCGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 168 NA -36 phiX2 + 3076 691 690 726 36 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 690 NA -35 phiX2 + 3076 2357 2356 2391 35 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2356 NA -36 phiX2 + 3076 1154 1153 1189 36 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1153 NA -35 phiX2 + 3076 2601 2600 2635 35 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TACACGCAGGACGCTTTTTCACGTTCTGGTTGGTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2600 NA -29 phiX2 + 3076 2282 2281 2310 29 GTTGGCTGACGACCGATTAGAGGCGTTTT HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 GTTGGCTGACGACCGATTAGAGGCGTTTT ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 2281 NA -25 phiX2 + 3076 575 574 607 33 TTATTAAAGAGATTATTTGTCTCCAGCCACTTA HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTATTAAAGAGATTATTTTTCTCCAGCCACTTA ..................x.............. 33M 32/33 97.0% 33/36 91.7% 0/33 0.0% 574 NA -36 phiX2 + 3076 2627 2626 2662 36 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2626 NA -34 phiX2 + 3076 2034 2033 2067 34 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA HWI-EAS91_1_306UPAAXX - 36 3 2 36 1 0 34 34 GAAAAATGGTTTTTAGAGAACGAGAAGACGGTTA .................................. 34M 34/34 100.0% 34/36 94.4% 0/34 0.0% 2031 NA -36 phiX2 + 3076 1364 1363 1399 36 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1363 NA -36 phiX2 + 3076 2635 2634 2670 36 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2634 NA -32 phiX2 + 3076 352 351 383 32 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCC HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 TGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCC ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 351 NA -36 phiX2 + 3076 1003 1002 1038 36 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1002 NA -25 phiX2 + 3076 517 516 549 33 ATGGTTTGGTCTAACTTTACCGCTACTAAATGC HWI-EAS91_1_306UPAAXX - 36 4 3 36 1 0 33 33 ATGGTTTGGTCAAACTTTACCGCTACTAAATGC ...........x..................... 33M 32/33 97.0% 33/36 91.7% 0/33 0.0% 513 NA -36 phiX2 + 3076 2626 2625 2661 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2625 NA -36 phiX2 + 3076 2695 2694 2730 36 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2694 NA -30 phiX2 + 3076 858 857 887 30 GGTAAAGGACTTCTTGAAGGTACGTTGCAG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 GGTAAAGGACTTCTTGAAGGTACGTTGCAG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 857 NA -33 phiX2 + 3076 428 427 460 33 GCCATGATGGTGGTTATTATACCGTCAAGGACT HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 GCCATGATGGTGGTTATTATACCGTCAAGGACT ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 427 NA -36 phiX2 + 3076 1789 1788 1824 36 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCTTGGCTTCCATAAGCAGATGGATAACCGCATCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1788 NA -36 phiX2 + 3076 264 263 299 36 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAGATGGATACATCTGTCAACGCCGCTAATCAGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 263 NA -36 phiX2 + 3076 143 142 178 36 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 142 NA -36 phiX2 + 3076 2869 2868 2904 36 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2868 NA -30 phiX2 + 3076 1468 1467 1497 30 TTTCTAATGTCGTCACTGATGCTGCTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 30 1 0 30 30 TTTCTAATGTCGTCACTGATGCTGCTTCTG .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 1467 NA -28 phiX2 + 3076 2327 2326 2362 36 TTTGCGTGACTATTTTCGTGATATTGGTCGTATGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTGCGTGACTATTTTCGTGATATTGTTCGTATGGT ..........................x......... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2326 NA -36 phiX2 + 3076 1058 1057 1093 36 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1057 NA -36 phiX2 + 3076 1001 1000 1036 36 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1000 NA -36 phiX2 + 3076 2729 2728 2764 36 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2728 NA -36 phiX2 + 3076 444 443 479 36 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATACCGTCAAGGACTGTGTGACTATTGACGTCCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 443 NA -36 phiX2 + 3076 1307 1306 1342 36 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1306 NA -36 phiX2 + 3076 418 417 453 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 417 NA -36 phiX2 + 3076 465 464 500 36 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GACTATTGACGTCCTTCCCCGTACGCCGGGCAATAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 464 NA -36 phiX2 + 3076 1907 1906 1942 36 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1906 NA -35 phiX2 + 3076 2309 2308 2343 35 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTATGATAATCCCAATGCTTTGCGTGACTATTTTC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2308 NA -35 phiX2 + 3076 420 419 454 35 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GAATGGTCGCCATGATGGTGGTTATTATACCGTCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 419 NA -36 phiX2 + 3076 1950 1949 1985 36 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAATGGATGAATTGGCACAATGCTACAATGTGCTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1949 NA -33 phiX2 + 3076 1864 1863 1896 33 TTGAGTTCGATAATGGTGATATGTATGTTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTGAGTTCGATAATGGTGATATGTATGTTGACG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1863 NA -36 phiX2 + 3076 2671 2670 2706 36 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2670 NA -35 phiX2 + 3076 11 10 45 35 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 10 NA -19 phiX2 + 3076 1874 1873 1908 35 TAATGGTGATATGTATGTTGACGGCCATAAGGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TAATGGTGATATGTATGTTTACGTCCATAAGGCTG ...................x...x........... 35M 33/35 94.3% 35/36 97.2% 0/35 0.0% 1873 NA -35 phiX2 + 3076 1778 1777 1812 35 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TCAATCCCCAATGCTTGGCTTCCATAAGCAGATGG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1777 NA -36 phiX2 + 3076 1277 1276 1312 36 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1276 NA -36 phiX2 + 3076 1477 1476 1512 36 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1476 NA -35 phiX2 + 3076 1524 1523 1558 35 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GATAAAGCTGTTGCCGATACTTGGAACAATTTCTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1523 NA -29 phiX2 + 3076 3048 3047 3076 29 ATAAAAATGATTGGCGTATCCAACCTGCA HWI-EAS91_1_306UPAAXX + 36 1 0 29 1 0 29 29 ATAAAAATGATTGGCGTATCCAACCTGCA ............................. 29M 29/29 100.0% 29/36 80.6% 0/29 0.0% 3047 29 -36 phiX2 + 3076 1402 1401 1437 36 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1401 NA -21 phiX2 + 3076 1990 1989 2010 21 AACTTGATATTAATAACACTA HWI-EAS91_1_306UPAAXX - 36 16 15 36 1 0 21 21 AACTTGATATTAATAACACTA ..................... 21M 21/21 100.0% 21/36 58.3% 0/21 0.0% 1974 NA -36 phiX2 + 3076 506 505 541 36 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 505 NA -36 phiX2 + 3076 2866 2865 2901 36 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2865 NA -36 phiX2 + 3076 1162 1161 1197 36 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGGCGACTTCACGCCAGAATACGAAAGACCAGGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1161 NA -35 phiX2 + 3076 1507 1506 1541 35 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 ATATTTTTCATGGTATTGATAAAGCTGTTGCCGAT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1506 NA -36 phiX2 + 3076 1253 1252 1288 36 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GTCTATTATGGAAAACACCAATCTTTCCAAGCAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1252 NA -35 phiX2 + 3076 1888 1887 1922 35 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1886 NA -35 phiX2 + 3076 597 596 631 35 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGC ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 595 NA -35 phiX2 + 3076 533 532 567 35 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TTACCGCTACTAAATGCCGCGGATTGGTTTCGCTG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 532 NA -31 phiX2 + 3076 2064 2063 2094 31 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 GTTACGCAGTTTTGCCGCAAGCTGGCTGCTG ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2063 NA -36 phiX2 + 3076 2763 2762 2798 36 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAATGGAACAACTCACTAAAAACCAAGCTGTCGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2762 NA -36 phiX2 + 3076 2124 2123 2159 36 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TATAATTACCCCAAAAAGAAAGGTATTAAGGATGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2123 NA -36 phiX2 + 3076 2130 2129 2165 36 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2129 NA -36 phiX2 + 3076 1610 1609 1645 36 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 GTCAGGATTGACACCCTCCCAATTGTATGTTTTCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1609 NA -35 phiX2 + 3076 2277 2276 2311 35 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CTCACGTTGGCTGACGACCGATTAGAGGCGTTTTA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2275 NA -24 phiX2 + 3076 1420 1419 1443 24 AGAATCAGCGGTATGGCTCTTCTC HWI-EAS91_1_306UPAAXX + 36 1 0 24 1 0 24 24 AGAATCAGCGGTATGGCTCTTCTC ........................ 24M 24/24 100.0% 24/36 66.7% 0/24 0.0% 1419 NA -36 phiX2 + 3076 388 387 423 36 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ACCCTCCCGACTGCCTATGATGTTTATCCTTTGAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 387 NA -36 phiX2 + 3076 857 856 892 36 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 856 NA -25 phiX2 + 3076 188 187 212 25 CTAAAGCTACATCGTCAACGTTATA HWI-EAS91_1_306UPAAXX - 36 12 11 36 1 0 25 25 CTAAAGCTACATCGTCAACGTTATA ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 176 NA -31 phiX2 + 3076 2705 2704 2735 31 TAAATACGTTAACAAAAAGTCAGATATGGAC HWI-EAS91_1_306UPAAXX - 36 6 5 36 1 0 31 31 TAAATACGTTAACAAAAAGTCAGATATGGAC ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2699 NA -36 phiX2 + 3076 2268 2267 2303 36 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTTGACACTCTCACGTTGGCTGACGACCGATTAGAG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2267 NA -36 phiX2 + 3076 1260 1259 1295 36 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1259 NA -30 phiX2 + 3076 2444 2443 2473 30 TAATGGCCGTCTTCATTTCCATGCGGTGCA HWI-EAS91_1_306UPAAXX - 36 1 0 30 7 6 36 30 TAATGGCCGTCTTCATTTCCATGCGGTGCA .............................. 30M 30/30 100.0% 30/36 83.3% 0/30 0.0% 2443 NA -35 phiX2 + 3076 1925 1924 1959 35 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGAGTTTGTATCTGTTACTGAGAAGTTAATGGATG ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1924 NA -31 phiX2 + 3076 1022 1021 1052 31 TGGTGCTGATGCTTCCTCTGCTGGTATGGTT HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 TGGTGCTGATGCTTCCTCTGCTGGTATGGTT ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 1021 NA -36 phiX2 + 3076 1822 1821 1857 36 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1821 NA -28 phiX2 + 3076 2465 2464 2500 36 TGCGGTGCACTTTATGCGGACACTTCCTACAGGTAG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGCGGTGCATTTTATGCGGACACTTCCTACAGGTAG .........:.......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2464 NA -36 phiX2 + 3076 1882 1881 1917 36 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATATGTATGTTGACGGCCATAAGGCTGCTTCTGACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1881 NA -35 phiX2 + 3076 2222 2221 2256 35 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 GATGAATGCAATGCGACAGGCTCATGCTGATGGTT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2220 NA -20 phiX2 + 3076 537 536 564 28 CGCTACTAAATGCCGCGGATTGGTTTCG HWI-EAS91_1_306UPAAXX + 36 5 4 32 5 4 32 28 CGCTACTAAATTCCGCGGATTGGTTTCG ...........x................ 28M 27/28 96.4% 28/36 77.8% 0/28 0.0% 532 NA -36 phiX2 + 3076 418 417 453 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTGAATGGTCGCCATGATGGTGGTTATTATACCGTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 417 NA -36 phiX2 + 3076 1669 1668 1704 36 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTATGGTTCGTTCTTATTACCCTTCTGAATGTCACG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1668 NA -36 phiX2 + 3076 2374 2373 2409 36 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGGTCGCAAGGCTAATGATTCACACGCCGACTGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2373 NA -32 phiX2 + 3076 1380 1379 1411 32 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCA HWI-EAS91_1_306UPAAXX + 36 1 0 32 1 0 32 32 AAGGTTAGTGCTGAGGTTGACTTAGTTCATCA ................................ 32M 32/32 100.0% 32/36 88.9% 0/32 0.0% 1379 NA -35 phiX2 + 3076 1542 1541 1576 35 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1540 NA -35 phiX2 + 3076 547 546 581 35 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 546 NA -26 phiX2 + 3076 1472 1471 1497 26 TAATGTCGTCACTGATGCTGCTTCTG HWI-EAS91_1_306UPAAXX + 36 1 0 26 1 0 26 26 TAATGTCGTCACTGATGCTGCTTCTG .......................... 26M 26/26 100.0% 26/36 72.2% 0/26 0.0% 1471 NA -35 phiX2 + 3076 2348 2347 2382 35 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 TATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2347 NA -36 phiX2 + 3076 132 131 167 36 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 131 NA -35 phiX2 + 3076 2816 2815 2850 35 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CAGAATCAGAATGAGCCGCAACTTCGGGATGAAAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2814 NA -36 phiX2 + 3076 2896 2895 2931 36 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2895 NA -36 phiX2 + 3076 569 568 604 36 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCAC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 568 NA -36 phiX2 + 3076 817 816 852 36 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 816 NA -36 phiX2 + 3076 1234 1233 1269 36 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1233 NA -31 phiX2 + 3076 198 197 228 31 ATCGTCAACGTTATATTTTGATAGTTTGACG HWI-EAS91_1_306UPAAXX + 36 1 0 31 1 0 31 31 ATCGTCAACGTTATATTTTGATAGTTTGACG ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 197 NA -16 phiX2 + 3076 788 787 811 24 TCAAGGCTCTAATGTTCCTAACCC HWI-EAS91_1_306UPAAXX - 36 13 12 36 1 0 24 24 TCAAGGCTCTAATGTCCCTAACCC ...............:........ 24M 23/24 95.8% 24/36 66.7% 0/24 0.0% 775 NA -36 phiX2 + 3076 1290 1289 1325 36 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1289 NA -33 phiX2 + 3076 345 344 377 33 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTC ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 344 NA -36 phiX2 + 3076 624 623 659 36 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 623 NA -36 phiX2 + 3076 1753 1752 1788 36 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1752 NA -36 phiX2 + 3076 1085 1084 1120 36 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1084 NA -33 phiX2 + 3076 1470 1469 1502 33 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTG HWI-EAS91_1_306UPAAXX + 36 1 0 33 1 0 33 33 TCTAATGTCGTCACTGATGCTGCTTCTGGTGTG ................................. 33M 33/33 100.0% 33/36 91.7% 0/33 0.0% 1469 NA -36 phiX2 + 3076 1672 1671 1707 36 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTG .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1671 NA -36 phiX2 + 3076 505 504 540 36 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 504 NA -35 phiX2 + 3076 2349 2348 2383 35 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 ATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 2347 NA -36 phiX2 + 3076 126 125 161 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 125 NA -28 phiX2 + 3076 2507 2506 2542 36 CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CCCTAATTTGGGTCGTCGGGTACGCAATCGCCGCCA .........x.......................... 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2506 NA -36 phiX2 + 3076 452 451 487 36 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 451 NA -36 phiX2 + 3076 2645 2644 2680 36 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2644 NA -36 phiX2 + 3076 1451 1450 1486 36 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CGCTACTGCAAAGGATATTTCTAATGTCGTCACTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1450 NA -28 phiX2 + 3076 2189 2188 2224 36 GAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGAT ...................:................ 36M 35/36 97.2% 36/36 100.0% 0/36 0.0% 2188 NA -36 phiX2 + 3076 1729 1728 1764 36 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1728 NA -36 phiX2 + 3076 2478 2477 2513 36 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCGGACACTTCCTACAGGTAGCGTTGACCCTAAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2477 NA -36 phiX2 + 3076 2071 2070 2106 36 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2070 NA -36 phiX2 + 3076 1946 1945 1981 36 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAAGTTAATGGATGAATTGGCACAATGCTACAATGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1945 NA -36 phiX2 + 3076 1552 1551 1587 36 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1551 NA +36 phiX2 + 3076 967 966 1002 36 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 966 NA 36 phiX2 + 3076 968 967 1003 36 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 967 NA -36 phiX2 + 3076 2298 2297 2333 36 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2297 NA -35 phiX2 + 3076 1498 1497 1532 35 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT HWI-EAS91_1_306UPAAXX + 36 1 0 35 1 0 35 35 GTGTGGTTGATATTTTTCATGGTATTGATAAAGCT ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 1497 NA -31 phiX2 + 3076 2443 2442 2473 31 CTAATGGCCGTCTTCATTTCCATGCGGTGCA HWI-EAS91_1_306UPAAXX - 36 1 0 31 6 5 36 31 CTAATGGCCGTCTTCATTTCCATGCGGTGCA ............................... 31M 31/31 100.0% 31/36 86.1% 0/31 0.0% 2442 NA -36 phiX2 + 3076 540 539 575 36 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 TACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 539 NA -36 phiX2 + 3076 2430 2429 2465 36 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 GAGTATGGTACAGCTAATGGCCGTCTTCATTTCCAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2429 NA -25 phiX2 + 3076 2345 2344 2369 25 TGATATTGGTCGTATGGTTCTTGCT HWI-EAS91_1_306UPAAXX + 36 1 0 25 1 0 25 25 TGATATTGGTCGTATGGTTCTTGCT ......................... 25M 25/25 100.0% 25/36 69.4% 0/25 0.0% 2344 NA -35 phiX2 + 3076 157 156 191 35 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA HWI-EAS91_1_306UPAAXX - 36 2 1 36 1 0 35 35 CCAGCTTCTTCGGCACCTGTTTTACAGACACCTAA ................................... 35M 35/35 100.0% 35/36 97.2% 0/35 0.0% 155 NA -36 phiX2 + 3076 446 445 481 36 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC HWI-EAS91_1_306UPAAXX + 36 1 0 36 1 0 36 36 ATACCGTCAAGGACTGTGTGACTATTGACGTCCTTC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 445 NA -36 phiX2 + 3076 2647 2646 2682 36 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 ATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 2646 NA -36 phiX2 + 3076 1939 1938 1974 36 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TTACTGAGAAGTTAATGGATGAATTGGCACAATGCT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1938 NA -36 phiX2 + 3076 282 281 317 36 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 281 NA -36 phiX2 + 3076 1230 1229 1265 36 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 AAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1229 NA -36 phiX2 + 3076 1820 1819 1855 36 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 CATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTAT .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 1819 NA +36 phiX2 + 3076 974 973 1009 36 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC HWI-EAS91_1_306UPAAXX - 36 1 0 36 1 0 36 36 TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGC .................................... 36M 36/36 100.0% 36/36 100.0% 0/36 0.0% 973 NA diff -r 60afd81f678b -r 658bfde702a1 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jan 11 12:07:58 2010 -0500 +++ b/test/base/twilltestcase.py Mon Jan 11 13:26:00 2010 -0500 @@ -36,12 +36,14 @@ #self.set_history() # Functions associated with files - def files_diff( self, file1, file2 ): + def files_diff( self, file1, file2, sort=False ): """Checks the contents of 2 files for differences""" if not filecmp.cmp( file1, file2 ): files_differ = False local_file = open( file1, 'U' ).readlines() history_data = open( file2, 'U' ).readlines() + if sort: + history_data.sort() if len( local_file ) == len( history_data ): for i in range( len( history_data ) ): if local_file[i].rstrip( '\r\n' ) != history_data[i].rstrip( '\r\n' ): @@ -520,7 +522,7 @@ hid = elem.get('hid') hids.append(hid) return hids - def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120 ): + def verify_dataset_correctness( self, filename, hid=None, wait=True, maxseconds=120, sort=False ): """Verifies that the attributes and contents of a history item meet expectations""" if wait: self.wait( maxseconds=maxseconds ) #wait for job to finish @@ -555,7 +557,7 @@ data = self.last_page() file( temp_name, 'wb' ).write(data) try: - self.files_diff( local_name, temp_name ) + self.files_diff( local_name, temp_name, sort=sort ) except AssertionError, err: os.remove(temp_name) errmsg = 'History item %s different than expected, difference:\n' % hid diff -r 60afd81f678b -r 658bfde702a1 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Mon Jan 11 12:07:58 2010 -0500 +++ b/test/functional/test_toolbox.py Mon Jan 11 13:26:00 2010 -0500 @@ -62,8 +62,8 @@ print "page_inputs (%i)" % i, page_inputs # Check the result assert len( testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet." - for name, file in testdef.outputs: - self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds ) + for name, file, sort in testdef.outputs: + self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds, sort=sort ) self.delete_history( id=self.security.encode_id( latest_history.id ) ) def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ): diff -r 60afd81f678b -r 658bfde702a1 tools/sr_mapping/lastz_wrapper.py --- a/tools/sr_mapping/lastz_wrapper.py Mon Jan 11 12:07:58 2010 -0500 +++ b/tools/sr_mapping/lastz_wrapper.py Mon Jan 11 13:26:00 2010 -0500 @@ -27,6 +27,7 @@ --identity_min: Minimum identity (don't report matches under this identity) --identity_max: Maximum identity (don't report matches above this identity) --coverage: The minimum coverage value (don't report matches covering less than this) + --unmask: Whether to convert lowercase bases to uppercase --out_format: The format of the output file (sam, diffs, or tabular (general)) --output: The name of the output file --lastzSeqsFileDir: Directory of local lastz_seqs.loc file @@ -145,11 +146,16 @@ parser.add_option( '', '--identity_min', dest='identity_min', help="Minimum identity (don't report matches under this identity)" ) parser.add_option( '', '--identity_max', dest='identity_max', help="Maximum identity (don't report matches above this identity)" ) parser.add_option( '', '--coverage', dest='coverage', help="The minimum coverage value (don't report matches covering less than this)" ) + parser.add_option( '', '--unmask', dest='unmask', help='Whether to convert lowercase bases to uppercase' ) parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' ) parser.add_option( '', '--output', dest='output', help='The output file' ) parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' ) ( options, args ) = parser.parse_args() + if options.unmask == 'yes': + unmask = '[unmask]' + else: + unmask = '' if options.ref_name != 'None': ref_name = '[nickname=%s]' % options.ref_name else: @@ -214,8 +220,8 @@ tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' ) os.close( tmp_out_fd ) # Generate the command line for calling lastz on the current sequence - command = 'lastz %s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s' % \ - ( tmp_in_name, ref_name, input2, set_options, options.identity_min, + command = 'lastz %s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s' % \ + ( tmp_in_name, unmask, ref_name, input2, set_options, options.identity_min, options.identity_max, options.coverage, format, tabular_fields, tmp_out_name ) # Create a job object job = Bunch() @@ -238,8 +244,8 @@ # Create a temporary file to contain the output from lastz execution on the current chrom tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' ) os.close( tmp_out_fd ) - command = 'lastz %s/%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \ - ( options.input1, chrom, ref_name, input2, set_options, options.identity_min, + command = 'lastz %s/%s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \ + ( options.input1, chrom, unmask, ref_name, input2, set_options, options.identity_min, options.identity_max, options.coverage, format, tabular_fields, tmp_out_name ) # Create a job object job = Bunch() diff -r 60afd81f678b -r 658bfde702a1 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Mon Jan 11 12:07:58 2010 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Mon Jan 11 13:26:00 2010 -0500 @@ -19,7 +19,7 @@ #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 --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} +--identity_min=$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" /> @@ -109,6 +109,10 @@ <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/> <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/> <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this percentage of each read"/> + <param name="unmask" type="select" label="Convert lowercase bases to uppercase"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> </inputs> <outputs> <data format="tabular" name="output1"> @@ -154,6 +158,7 @@ <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> + <param name="unmask" value="yes" /> <output name="output1" file="lastz_wrapper_out2.sam" /> </test> <test> @@ -173,6 +178,7 @@ <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> + <param name="unmask" value="yes" /> <output name="output1" file="lastz_wrapper_out3.tabular" /> </test> <test> @@ -185,6 +191,9 @@ phiX_split.fasta and b1.fasta are located in galaxy's test-data You will have to replace all the asterisks before the commands with 2 dashes, as double-dash can't appear in an XML comment + + NOTE: since the input file include more than 1 sequence, the output must be sorted in + order for functional test to pass. This is done using the sort="True" attribute on the output. --> <param name="input2" value="b1.fasta" ftype="fasta" /> <param name="ref_source" value="history" /> @@ -196,14 +205,17 @@ <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> - <output name="output1" file="lastz_wrapper_out4.tabular" /> + <param name="unmask" value="yes" /> + <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" /> </test> </tests> <help> **What it does** -**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. +**LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. The Galaxy version of LASTZ is geared towards aligning of short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive `documentation`__ on LASTZ available, although it hasn't been updated for the version of LASTZ that Galaxy is running (the key changes have to do with output formats, so it is still extremely helpful). + + .. __: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.0… ------ @@ -215,26 +227,34 @@ **Outputs** -LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a list of pairwise alignments in MAF format. Examples of these outputs are shown below. +LASTZ generates one output. Depending on the choice you make in *Select output format* drop-down LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below. **SAM output** -SAM has the following columns:: +SAM has 12 columns:: - Column Description - -------- -------------------------------------------------------- - 1 QNAME Query (pair) NAME - 2 FLAG bitwise FLAG - 3 RNAME Reference sequence NAME - 4 POS 1-based leftmost POSition/coordinate of clipped sequence - 5 MAPQ MAPping Quality (Phred-scaled) - 6 CIGAR extended CIGAR string - 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) - 8 MPOS 1-based Mate POSition - 9 ISIZE Inferred insert SIZE - 10 SEQ query SEQuence on the same strand as the reference - 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) - 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE + 1 2 3 4 5 6 7 8 9 10 11 12 + ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 + HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 + + +where:: + + Column Description + --------- --------------------------------------------------------------------- + 1. QNAME Query (pair) NAME + 2. FLAG bitwise FLAG + 3. RNAME Reference sequence NAME + 4. POS 1-based leftmost POSition/coordinate of clipped sequence + 5. MAPQ MAPping Quality (Phred-scaled) + 6. CIGAR extended CIGAR string + 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME) + 8. MPOS 1-based Mate POSition + 9. ISIZE Inferred insert SIZE + 10. SEQ query SEQuence on the same strand as the reference + 11. QUAL query QUALity (ASCII-33 gives the Phred base quality) + 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated The flags are as follows:: @@ -250,19 +270,9 @@ 0x0080 the read is the second read in a pair 0x0100 the alignment is not primary -It looks like this (scroll sideways to see the entire example):: - - QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT - HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh - HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh - -**Suppress SAM headers in output** - -Choose whether or not to suppress SAM headers. - **Polymorphism (SNP or differences) output** -Polymorphism output contains 14 columns (scroll sideways to see the entire example):: +Polymorphism output contains 14 columns:: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 -------------------------------------------------------------------------------------------------------------------------------------------------------------- @@ -286,21 +296,46 @@ 13. (ACC...) - Reference side os the alignment 14. (ACC...) - Read side of the alignment -**MAF output** +**Tabular output** -Multiple alignment output conforms to the MAF format used by mitliZ, TBA and other multiple aligners. This is the format used extensively by UCSC Genome Biology Group:: +Tabular output is a tab-separated format with 30 columns:: - a score=35 - s chrM 4294 35 + 5386 CCCCCAACTTGATATTAATAACACTATAGACCACC - s read 1 35 - 36 CCCCCAACTTGATATTAATAACACTATAGACCACC + 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 + ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA + 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA - a score=36 - s chrM 3521 36 + 5386 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC - s read 0 36 - 36 ATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGC - -.. class:: infomark +The following columns are present:: -MAF output format of LASTZ strips read names and replaces them with *read* label. + Field Meaning + ---------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options. + 2. name1 Name of the target sequence. + 3. strand1 Target sequence strand, either "+" or "−". + 4. size1 Size of the entire target sequence. + 5. start1 Starting position of the alignment block in the target, origin-one. + 6. zstart1 Starting position of the alignment block in the target, origin-zero. + 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). + 8. length1 Length of the alignment block in the target (excluding gaps). + 9. text1 Aligned characters in the target, including gap characters. + 10. name2 Name of the query sequence. + 11. strand2 Query sequence strand, either "+" or "−". + 12. size2 Size of the entire query sequence. + 13. start2 Starting position of the alignment block in the query, origin-one. + 14. zstart2 Starting position of the alignment block in the query, origin-zero. + 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). + 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2. + 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2. + 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2. + 19. length2 Length of the alignment block in the query (excluding gaps). + 20. text2 Aligned characters in the query, including gap characters. + 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen). + 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification. + 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage. + 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage. + 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage. + 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2. + 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap. -------

1 0

[hg] galaxy 3222: Check / uncheck all in create workflow from hi...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/60afd81f678b changeset: 3222:60afd81f678b user: James Taylor <james(a)jamestaylor.org> date: Mon Jan 11 12:07:58 2010 -0500 description: Check / uncheck all in create workflow from history, also made template extend base since I was already mcuking with it diffstat: templates/workflow/build_from_current_history.mako | 69 ++++++++++++--------- 1 files changed, 39 insertions(+), 30 deletions(-) diffs (93 lines): diff -r 6127f0928166 -r 60afd81f678b templates/workflow/build_from_current_history.mako --- a/templates/workflow/build_from_current_history.mako Fri Jan 08 16:22:44 2010 -0500 +++ b/templates/workflow/build_from_current_history.mako Mon Jan 11 12:07:58 2010 -0500 @@ -1,31 +1,40 @@ +<%inherit file="/base.mako"/> + <% _=n_ %> - -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html> +<%def name="title()">Extract workflow from history</%def> -<head> -<title>Galaxy</title> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<link href="${h.url_for('/static/style/history.css')}" rel="stylesheet" type="text/css" /> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> +<%def name="stylesheets()"> + ${h.css( 'history', 'base' )} + <style type="text/css"> + div.toolForm{ + margin-top: 10px; + margin-bottom: 10px; + } + div.historyItem { + margin-right: 0; + } + th { + border-bottom: solid black 1px; + } + </style> +</%def> -<style type="text/css"> -div.toolForm{ - margin-top: 10px; - margin-bottom: 10px; -} -div.historyItem { - margin-right: 0; -} -th { - border-bottom: solid black 1px; -} -</style> - -</head> - -<body> +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function() { + $("#checkall").click( function() { + $("input[type=checkbox]").attr( 'checked', true ); + return false; + }).show(); + $("#uncheckall").click( function() { + $("input[type=checkbox]").attr( 'checked', false ); + return false; + }).show(); + }); + </script> +</%def> <%def name="history_item( data, creator_disabled=False )"> %if data.state in [ "no state", "", None ]: @@ -71,7 +80,11 @@ <label>${_('Workflow name')}</label> <input name="workflow_name" type="text" value="Workflow constructed from history '${history.name}'" size="60"/> </div> -<p><input type="submit" value="${_('Create Workflow')}" /></p> +<p> + <input type="submit" value="${_('Create Workflow')}" /> + <button id="checkall" style="display: none;">Check all</button> + <button id="uncheckall" style="display: none;">Uncheck all</button> +</p> <table border="0" cellspacing="0"> @@ -127,8 +140,4 @@ </table> -</form> - -</body> - -</html> \ No newline at end of file +</form> \ No newline at end of file

1 0

[hg] galaxy 3221: Enhance lastz to better handle files with many...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6127f0928166 changeset: 3221:6127f0928166 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jan 08 16:22:44 2010 -0500 description: Enhance lastz to better handle files with many sequences. diffstat: tools/sr_mapping/lastz_wrapper.py | 194 ++++++++++++++++++++++-------------- tools/sr_mapping/lastz_wrapper.xml | 18 +-- 2 files changed, 127 insertions(+), 85 deletions(-) diffs (343 lines): diff -r b4f1f54ced6a -r 6127f0928166 tools/sr_mapping/lastz_wrapper.py --- a/tools/sr_mapping/lastz_wrapper.py Fri Jan 08 11:28:37 2010 -0500 +++ b/tools/sr_mapping/lastz_wrapper.py Fri Jan 08 16:22:44 2010 -0500 @@ -29,10 +29,9 @@ --coverage: The minimum coverage value (don't report matches covering less than this) --out_format: The format of the output file (sam, diffs, or tabular (general)) --output: The name of the output file - --num_threads: The number of threads to run --lastzSeqsFileDir: Directory of local lastz_seqs.loc file """ -import optparse, os, subprocess, shutil, sys, tempfile, threading +import optparse, os, subprocess, shutil, sys, tempfile, threading, time from Queue import Queue from galaxy import eggs @@ -40,39 +39,86 @@ pkg_resources.require( 'bx-python' ) from bx.seq.twobit import * from bx.seq.fasta import FastaReader +from galaxy.util.bunch import Bunch + +STOP_SIGNAL = object() +WORKERS = 4 +SLOTS = 128 def stop_err( msg ): sys.stderr.write( "%s" % msg ) sys.exit() -class LastzJobRunner( object ): - """ - Lastz job runner backed by a pool of "num_threads" worker threads. FIFO scheduling - """ - def __init__( self, num_threads, commands ): - """Start the job runner with "num_threads" worker threads""" - # start workers - self.queue = Queue() - for command in commands: - self.queue.put( command ) +def stop_queues( lastz, combine_data ): + # This method should only be called if an error has been encountered. + # Send STOP_SIGNAL to all worker threads + for t in lastz.threads: + lastz.put( STOP_SIGNAL, True ) + combine_data.put( STOP_SIGNAL, True ) + +class BaseQueue( object ): + def __init__( self, num_threads, slots=-1 ): + # Initialize the queue and worker threads + self.queue = Queue( slots ) self.threads = [] for i in range( num_threads ): worker = threading.Thread( target=self.run_next ) worker.start() self.threads.append( worker ) - for worker in self.threads: - worker.join() def run_next( self ): - """Run the next command, waiting until one is available if necessary""" - while not self.queue.empty(): - command = self.queue.get() - self.run_job( command ) - def run_job( self, command ): - try: - proc = subprocess.Popen( args=command, shell=True ) - proc.wait() - except Exception, e: - stop_err( "Error executing command (%s) - %s" % ( str( command ), str( e ) ) ) + # Run the next job, waiting until one is available if necessary + while True: + job = self.queue.get() + if job is STOP_SIGNAL: + return self.shutdown() + self.run_job( job ) + time.sleep( 1 ) + def run_job( self, job ): + stop_err( 'Not Implemented' ) + def put( self, job, block=False ): + # Add a job to the queue + self.queue.put( job, block ) + def shutdown( self ): + return + +class LastzJobQueue( BaseQueue ): + """ + A queue that runs commands in parallel. Blocking is done so the queue will + not consume much memory. + """ + def run_job( self, job ): + # Execute the job's command + proc = subprocess.Popen( args=job.command, shell=True, stderr=subprocess.PIPE, ) + proc.wait() + stderr = proc.stderr.read() + proc.wait() + if stderr: + stop_queues( self, job.combine_data_queue ) + stop_err( stderr ) + job.combine_data_queue.put( job ) + +class CombineDataQueue( BaseQueue ): + """ + A queue that concatenates files in serial. Blocking is not done since this + queue is not expected to grow larger than the command queue. + """ + def __init__( self, output_filename, num_threads=1 ): + BaseQueue.__init__( self, num_threads ) + self.CHUNK_SIZE = 2**20 # 1Mb + self.output_file = open( output_filename, 'wb' ) + def run_job( self, job ): + in_file = open( job.output, 'rb' ) + while True: + chunk = in_file.read( self.CHUNK_SIZE ) + if not chunk: + in_file.close() + break + self.output_file.write( chunk ) + for file_name in job.cleanup: + os.remove( file_name ) + def shutdown( self ): + self.output_file.close() + return def __main__(): #Parse Command Line @@ -101,17 +147,9 @@ parser.add_option( '', '--coverage', dest='coverage', help="The minimum coverage value (don't report matches covering less than this)" ) parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' ) parser.add_option( '', '--output', dest='output', help='The output file' ) - parser.add_option( '', '--num_threads', dest='num_threads', help='The number of threads to run' ) parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' ) ( options, args ) = parser.parse_args() - # If the reference sequences are from the history, temporary input files will be created - # ( 1 for each sequence ), and we'll keep track of them for later removal from disk ( by closing them ) - tmp_in_file_names = [] - # Each thread will create a temporary file to which it writes the output from lastz - tmp_out_file_names = [] - # Execution of lastz based on job splitting - commands = [] if options.ref_name != 'None': ref_name = '[nickname=%s]' % options.ref_name else: @@ -122,9 +160,8 @@ # Prepare for user-specified options else: set_options = '--%s --%s --gapped --strand=%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \ - ( options.gfextend, options.chain, options.strand, options.seed, - options.transition, options.O, options.E, options.X, - options.Y, options.K, options.L, options.entropy ) + ( options.gfextend, options.chain, options.strand, options.seed, options.transition, + options.O, options.E, options.X, options.Y, options.K, options.L, options.entropy ) # Specify input2 and add [fullnames] modifier if output format is diffs if options.format == 'diffs': input2 = '%s[fullnames]' % options.input2 @@ -141,15 +178,23 @@ else: format = options.format tabular_fields = '' + + # Set up our queues + lastz_job_queue = LastzJobQueue( WORKERS, slots=SLOTS ) + combine_data_queue = CombineDataQueue( options.output ) + if options.ref_source == 'history': - # Reference is a fasta dataset from the history, so split job across number of sequences in the dataset + # Reference is a fasta dataset from the history, so split job across + # the number of sequences in the dataset ( this could be a HUGE number ) try: # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ). error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes." ref_sequences = int( options.ref_sequences ) if ref_sequences < 1: + stop_queues( lastz_job_queue, combine_data_queue ) stop_err( error_msg ) except: + stop_queues( lastz_job_queue, combine_data_queue ) stop_err( error_msg ) seqs = 0 fasta_reader = FastaReader( open( options.input1 ) ) @@ -160,60 +205,61 @@ break seqs += 1 # Create a temporary file to contain the current sequence as input to lastz - tmp_in = tempfile.NamedTemporaryFile( prefix=seq.name, suffix='.fasta' ) - tmp_in_name = tmp_in.name - tmp_in.close() - tmp_in = file(tmp_in_name,'w+b') - # Keep track of our list of temporary input files so we can remove them later by closing them - tmp_in_file_names.append( tmp_in_name ) + tmp_in_fd, tmp_in_name = tempfile.mkstemp( suffix='.in' ) + tmp_in = os.fdopen( tmp_in_fd, 'wb' ) # Write the current sequence to the temporary input file tmp_in.write( '>%s\n%s\n' % ( seq.name, seq.text ) ) tmp_in.close() # Create a 2nd temporary file to contain the output from lastz execution on the current sequence - tmp_out = tempfile.NamedTemporaryFile( prefix='%s_out' % seq.name ) - tmp_out_name = tmp_out.name - tmp_out.close() - # Keep track of our list of temporary output files so we can merge them into our output dataset - tmp_out_file_names.append( tmp_out_name ) + tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' ) + os.close( tmp_out_fd ) # Generate the command line for calling lastz on the current sequence command = 'lastz %s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s' % \ ( tmp_in_name, ref_name, input2, set_options, options.identity_min, options.identity_max, options.coverage, format, tabular_fields, tmp_out_name ) - # Append the command line to our list of commands for sending to the LastzJobRunner queue - commands.append( command ) - # Make sure the value of sequences in the metadata is the - # same as the number of sequences read from the dataset ( this may not be necessary ). + # Create a job object + job = Bunch() + job.command = command + job.output = tmp_out_name + job.cleanup = [ tmp_in_name, tmp_out_name ] + job.combine_data_queue = combine_data_queue + # Add another job to the lastz_job_queue. Execution + # will wait at this point if the queue is full. + lastz_job_queue.put( job, block=True ) + # Make sure the value of sequences in the metadata is the same as the + # number of sequences read from the dataset ( this may not be necessary ). if ref_sequences != seqs: - stop_error( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference ( %d)." % ( ref_sequences, seqs ) ) + stop_queues( lastz_job_queue, combine_data_queue ) + stop_err( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference ( %d)." % ( ref_sequences, seqs ) ) else: # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file tbf = TwoBitFile( open( options.input1, 'r' ) ) for chrom in tbf.keys(): # Create a temporary file to contain the output from lastz execution on the current chrom - tmp_out = tempfile.NamedTemporaryFile( prefix='%s_out' % chrom ) - tmp_out_name = tmp_out.name - tmp_out.close() - # Keep track of our list of temporary output files so we can merge them into our output dataset - tmp_out_file_names.append( tmp_out_name ) + tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' ) + os.close( tmp_out_fd ) command = 'lastz %s/%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \ ( options.input1, chrom, ref_name, input2, set_options, options.identity_min, options.identity_max, options.coverage, format, tabular_fields, tmp_out_name ) - commands.append( command ) - job_runner = LastzJobRunner( int( options.num_threads ), commands ) - # Merge all of the output from lastz ( currently in temporary files ) into our output dataset - command = 'cat %s >> %s' % ( ' '.join( tmp_out_file_names ), options.output ) - proc = subprocess.Popen( args=command, shell=True ) - proc.wait() - # Remove all temporary files from disk by closing them - for name in tmp_in_file_names: - try: - os.remove( name ) - except: - pass - for name in tmp_out_file_names: - try: - os.remove( name ) - except: - pass + # Create a job object + job = Bunch() + job.command = command + job.output = tmp_out_name + job.cleanup = [ tmp_out_name ] + job.combine_data_queue = combine_data_queue + # Add another job to the lastz_job_queue. Execution + # will wait at this point if the queue is full. + lastz_job_queue.put( job, block=True ) + + # Stop the lastz_job_queue + for t in lastz_job_queue.threads: + lastz_job_queue.put( STOP_SIGNAL, True ) + # Although all jobs are submitted to the queue, we can't shut down the combine_data_queue + # until we know that all jobs have been submitted to its queue. We do this by checking + # whether all of the threads in the lastz_job_queue have terminated. + while threading.activeCount() > 2: + time.sleep( 1 ) + # Now it's safe to stop the combine_data_queue + combine_data_queue.put( STOP_SIGNAL ) if __name__=="__main__": __main__() diff -r b4f1f54ced6a -r 6127f0928166 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml Fri Jan 08 11:28:37 2010 -0500 +++ b/tools/sr_mapping/lastz_wrapper.xml Fri Jan 08 16:22:44 2010 -0500 @@ -19,7 +19,7 @@ #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 --num_threads=$num_threads --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} +--identity_min=$min_ident --identity_max=$max_ident --coverage=$min_cvrg --output=$output1 --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR} </command> <inputs> <param name="input2" format="fasta" type="data" label="Align sequencing reads in" /> @@ -109,10 +109,6 @@ <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/> <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/> <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this percentage of each read"/> - <param name="num_threads" type="select" label="Number of threads" help="Split this job over the selected number of threads"> - <option value="4">4</option> - <option value="8">8</option> - </param> </inputs> <outputs> <data format="tabular" name="output1"> @@ -149,14 +145,15 @@ <param name="K" value="3000" /> <param name="L" value="3000" /> <param name="entropy" value="noentropy" /> -  +  <param name="how_to_name" value="yes" /> <param name="ref_name" value="Ref" /> <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> - <param name="num_threads" value="4" /> <output name="output1" file="lastz_wrapper_out2.sam" /> </test> <test> @@ -176,11 +173,10 @@ <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> - <param name="num_threads" value="4" /> <output name="output1" file="lastz_wrapper_out3.tabular" /> </test> - <test> - <!-- + <test> + <!-- Lastz command: first you will need to split the file phiX_split.fasta into two files, phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then: lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular @@ -200,7 +196,6 @@ <param name="min_ident" value="0" /> <param name="max_ident" value="100" /> <param name="min_cvrg" value="0" /> - <param name="num_threads" value="4" /> <output name="output1" file="lastz_wrapper_out4.tabular" /> </test> </tests>

1 0

[hg] galaxy 3220: Fixed functional tests for short_reads_figure_...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b4f1f54ced6a changeset: 3220:b4f1f54ced6a user: gua110 date: Fri Jan 08 11:28:37 2010 -0500 description: Fixed functional tests for short_reads_figure_score tool. diffstat: test-data/454Score.png | 0 test-data/solexaScore.png | 0 tools/metag_tools/short_reads_figure_score.xml | 2 +- 3 files changed, 1 insertions(+), 1 deletions(-) diffs (13 lines): diff -r 195161a630bd -r b4f1f54ced6a test-data/454Score.png Binary file test-data/454Score.png has changed diff -r 195161a630bd -r b4f1f54ced6a test-data/solexaScore.png Binary file test-data/solexaScore.png has changed diff -r 195161a630bd -r b4f1f54ced6a tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml Thu Jan 07 18:48:38 2010 -0500 +++ b/tools/metag_tools/short_reads_figure_score.xml Fri Jan 08 11:28:37 2010 -0500 @@ -1,4 +1,4 @@ -<tool id="quality_score_distribution" name="Build base quality distribution" version="1.0.1"> +<tool id="quality_score_distribution" name="Build base quality distribution" version="1.0.2"> <description></description> <command interpreter="python">short_reads_figure_score.py $input1 $output1 </command>

1 0

[hg] galaxy 3219: Add missing bam provider
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/195161a630bd changeset: 3219:195161a630bd user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 07 18:48:38 2010 -0500 description: Add missing bam provider diffstat: lib/galaxy/visualization/tracks/data/bam.py | 24 ++++++++++++++++++++++++ 1 files changed, 24 insertions(+), 0 deletions(-) diffs (29 lines): diff -r 9ed3e27a6e4c -r 195161a630bd lib/galaxy/visualization/tracks/data/bam.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/data/bam.py Thu Jan 07 18:48:38 2010 -0500 @@ -0,0 +1,24 @@ +import pkg_resources; pkg_resources.require( "pysam" ) +from pysam import csamtools +from math import floor, ceil, log +import logging + +class BamDataProvider( object ): + def __init__( self, index, original_dataset ): + self.log = logging.getLogger(__name__) + self.index = index + self.original_dataset = original_dataset + + def get_data( self, chrom, start, end, **kwargs ): + start, end = int(start), int(end) + bamfile = csamtools.Samfile(filename=self.original_dataset.file_name, mode='rb', index_filename=self.index.file_name) + + data = bamfile.fetch(start=start, end=end, reference=chrom) + results = [] + for read in data: + payload = { 'uid': str(read.pos) + str(read.seq), 'start': read.pos, 'end': read.pos + read.rlen, 'name': read.seq } + + results.append(payload) + bamfile.close() + return results + \ No newline at end of file

1 0

[hg] galaxy 3218: Add bam_to_bai converter
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9ed3e27a6e4c changeset: 3218:9ed3e27a6e4c user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 07 17:52:08 2010 -0500 description: Add bam_to_bai converter diffstat: lib/galaxy/datatypes/converters/bam_to_bai.xml | 13 +++++++++++++ 1 files changed, 13 insertions(+), 0 deletions(-) diffs (18 lines): diff -r 62c7260e7fb7 -r 9ed3e27a6e4c lib/galaxy/datatypes/converters/bam_to_bai.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/bam_to_bai.xml Thu Jan 07 17:52:08 2010 -0500 @@ -0,0 +1,13 @@ +<tool id="INDEXER_Bam_Bai_0" name="Bam to Bai"> + <command>samtools index $input $output</command> + <inputs> + <page> + <param format="bam" name="input" type="data" label="Choose BAM"/> + </page> + </inputs> + <outputs> + <data format="bai" name="output"/> + </outputs> + <help> + </help> +</tool> \ No newline at end of file

1 0

[hg] galaxy 3217: Fix accidentally committed fastx tool configs
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/62c7260e7fb7 changeset: 3217:62c7260e7fb7 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Jan 07 16:20:04 2010 -0500 description: Fix accidentally committed fastx tool configs diffstat: tools/fastx_toolkit/fastq_to_fasta.xml | 2 +- tools/fastx_toolkit/fastx_collapser.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diffs (22 lines): diff -r 7d3667e8e415 -r 62c7260e7fb7 tools/fastx_toolkit/fastq_to_fasta.xml --- a/tools/fastx_toolkit/fastq_to_fasta.xml Thu Jan 07 15:45:15 2010 -0500 +++ b/tools/fastx_toolkit/fastq_to_fasta.xml Thu Jan 07 16:20:04 2010 -0500 @@ -1,6 +1,6 @@ <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA"> <description>converter</description> - <command>gunzip -cf $input | fastq_to_fasta -Q 33 $SKIPN $RENAMESEQ -o $output -v </command> + <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command> <inputs> <param format="fastq" name="input" type="data" label="FASTQ Library to convert" /> diff -r 7d3667e8e415 -r 62c7260e7fb7 tools/fastx_toolkit/fastx_collapser.xml --- a/tools/fastx_toolkit/fastx_collapser.xml Thu Jan 07 15:45:15 2010 -0500 +++ b/tools/fastx_toolkit/fastx_collapser.xml Thu Jan 07 16:20:04 2010 -0500 @@ -1,6 +1,6 @@ <tool id="cshl_fastx_collapser" name="Collapse"> <description>sequences</description> - <command>zcat -f '$input' | fastx_collapser -Q 33 -v -o '$output' </command> + <command>zcat -f '$input' | fastx_collapser -v -o '$output' </command> <inputs> <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" />

1 0

[hg] galaxy 3216: trackster: support BAM visualization with samt...
by Greg Von Kuster 12 Jan '10

12 Jan '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7d3667e8e415 changeset: 3216:7d3667e8e415 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Jan 07 15:45:15 2010 -0500 description: trackster: support BAM visualization with samtools, automatically enable tracks for any datatype with "get_track_type" defined diffstat: datatypes_conf.xml.sample | 4 +- eggs.ini | 2 + lib/galaxy/datatypes/binary.py | 4 +- lib/galaxy/datatypes/coverage.py | 2 - lib/galaxy/datatypes/interval.py | 7 +- lib/galaxy/datatypes/registry.py | 8 ++- lib/galaxy/web/controllers/tracks.py | 38 ++++++-------- static/scripts/packed/galaxy.panels.js | 2 +- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 88 +++++++++++++++++++++++++++++---- templates/tracks/browser.mako | 2 +- templates/tracks/new_browser.mako | 4 +- 12 files changed, 117 insertions(+), 46 deletions(-) diffs (439 lines): diff -r 427d93bf3d39 -r 7d3667e8e415 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Jan 07 14:52:51 2010 -0500 +++ b/datatypes_conf.xml.sample Thu Jan 07 15:45:15 2010 -0500 @@ -3,7 +3,9 @@ <registration converters_path="lib/galaxy/datatypes/converters"> <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> - <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> + <converter file="bam_to_bai.xml" target_datatype="bai"/> + </datatype> <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> <converter file="interval_to_coverage.xml" target_datatype="coverage"/> diff -r 427d93bf3d39 -r 7d3667e8e415 eggs.ini --- a/eggs.ini Thu Jan 07 14:52:51 2010 -0500 +++ b/eggs.ini Thu Jan 07 15:45:15 2010 -0500 @@ -19,6 +19,7 @@ pbs_python = 2.9.4 psycopg2 = 2.0.6 pycrypto = 2.0.1 +pysam = 0.1.1 pysqlite = 2.5.6 python_lzo = 1.08 threadframe = 0.2 @@ -74,6 +75,7 @@ pbs_python = http://ftp.sara.nl/pub/outgoing/pbs_python-2.9.4.tar.gz psycopg2 = http://initd.org/pub/software/psycopg/PSYCOPG-2-0/psycopg2-2.0.6.tar.gz ftp://ftp-archives.postgresql.org/pub/source/v8.2.6/postgresql-8.2.6.tar.bz2 pycrypto = http://www.amk.ca/files/python/crypto/pycrypto-2.0.1.tar.gz +pysam = http://bitbucket.org/kanwei/kanwei-pysam/get/e3c601a062fd.gz pysqlite = http://pypi.python.org/packages/source/p/pysqlite/pysqlite-2.5.6.tar.gz python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar… http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/binary.py Thu Jan 07 15:45:15 2010 -0500 @@ -132,7 +132,9 @@ return dataset.peek except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) - + def get_track_type( self ): + return "ReadTrack", "bai" + class Binseq( Binary ): """Class describing a zip archive of binary sequence files""" file_ext = "binseq.zip" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/coverage.py --- a/lib/galaxy/datatypes/coverage.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/coverage.py Thu Jan 07 15:45:15 2010 -0500 @@ -63,6 +63,4 @@ resolution = max( resolution, 1 ) return resolution - def get_track_type( self ): - return "LineTrack" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/interval.py Thu Jan 07 15:45:15 2010 -0500 @@ -325,8 +325,6 @@ def get_track_resolution( self, dataset, start, end): return None - def get_track_type( self ): - return "FeatureTrack" class Bed( Interval ): """Tab delimited data in BED format""" @@ -484,6 +482,9 @@ else: return False return True except: return False + + def get_track_type( self ): + return "FeatureTrack", "interval_index" class _RemoteCallMixin: def _get_remote_call_url( self, redirect_url, site_name, dataset, type, app, base_url ): @@ -904,7 +905,7 @@ resolution = max( resolution, 1 ) return resolution def get_track_type( self ): - return "LineTrack" + return "LineTrack", "array_tree" class CustomTrack ( Tabular ): """UCSC CustomTrack""" diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/datatypes/registry.py Thu Jan 07 15:45:15 2010 -0500 @@ -18,6 +18,7 @@ self.datatype_converters = odict() self.datatype_indexers = odict() self.converters = [] + self.available_tracks = [] self.set_external_metadata_tool = None self.indexers = [] self.sniff_order = [] @@ -54,6 +55,8 @@ # Use default mime type as per datatype spec mimetype = self.datatypes_by_extension[extension].get_mime() self.mimetypes_by_extension[extension] = mimetype + if hasattr( getattr( module, datatype_class ), "get_track_type" ): + self.available_tracks.append( extension ) if display_in_upload: self.upload_file_formats.append( extension ) for converter in elem.findall( 'converter' ): @@ -206,7 +209,10 @@ if not included: self.sniff_order.append(datatype) append_to_sniff_order() - + + def get_available_tracks(self): + return self.available_tracks + def get_mimetype_by_extension(self, ext ): """Returns a mimetype based on an extension""" try: diff -r 427d93bf3d39 -r 7d3667e8e415 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Jan 07 14:52:51 2010 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Jan 07 15:45:15 2010 -0500 @@ -23,35 +23,26 @@ from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider from galaxy.visualization.tracks.data.interval_index import IntervalIndexDataProvider +from galaxy.visualization.tracks.data.bam import BamDataProvider # Message strings returned to browser messages = Bunch( PENDING = "pending", NO_DATA = "no data", NO_CHROMOSOME = "no chromosome", + NO_CONVERTER = "no converter", DATA = "data", ERROR = "error" ) -# Dataset type required for each track type. This needs to be more flexible, -# there might be multiple types of indexes that suffice for a given track type. -track_type_to_dataset_type = { - "line": "array_tree", - "feature": "interval_index" -} - # Mapping from dataset type to a class that can fetch data from a file of that # type. This also needs to be more flexible. dataset_type_to_data_provider = { "array_tree": ArrayTreeDataProvider, - "interval_index": IntervalIndexDataProvider + "interval_index": IntervalIndexDataProvider, + "bai": BamDataProvider } -# FIXME: hardcoding this for now, but it should be derived from the available -# converters -browsable_types = ( "wig", "bed" ) - - class TracksController( BaseController ): """ Controller for track browser interface. Handles building a new browser from @@ -107,11 +98,12 @@ # Find all datasets in the current history that are of that dbkey # and can be displayed datasets = {} + available_tracks = trans.app.datatypes_registry.get_available_tracks() for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: + if dataset.metadata.dbkey == dbkey and dataset.extension in available_tracks: datasets[dataset.id] = (dataset.extension, dataset.name) # Render the template - return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + return trans.fill_template( "tracks/new_browser.mako", available_tracks=available_tracks, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose def browser(self, trans, id, chrom=""): @@ -127,8 +119,10 @@ for t in vis.latest_revision.config['tracks']: dataset_id = t['dataset_id'] dataset = hda_query.get( dataset_id ) + track_type, indexer = dataset.datatype.get_track_type() tracks.append( { - "type": dataset.datatype.get_track_type(), + "type": track_type, + "indexer": indexer, "name": dataset.name, "dataset_id": dataset.id } ) @@ -184,14 +178,14 @@ return manifest @web.json - def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ): + def data( self, trans, dataset_id, indexer, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ # Load the requested dataset dataset = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) # No dataset for that id - if not dataset: + if not dataset or not chrom: return messages.NO_DATA # Dataset is in error state, can't display if dataset.state == trans.app.model.Job.states.ERROR: @@ -200,12 +194,11 @@ if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING # Determine what to return based on the type of track being drawn. - converted_dataset_type = track_type_to_dataset_type[track_type] + converted_dataset_type = indexer converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) - # If at this point we still don't have an `array_tree_dataset`, there - # is no way we can display this data as an array tree if not converted_dataset: - return messages.ERROR + # No converter + return messages.NO_CONVERTER # Need to check states again for the converted version if converted_dataset.state == model.Dataset.states.ERROR: return messages.ERROR @@ -228,6 +221,7 @@ converted dataset (possibly new) is returned, if it cannot be converted, None is returned. """ + log.debug("Inside dataset as type") # Already of correct type if dataset.extension == type: return dataset diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Thu Jan 07 14:52:51 2010 -0500 +++ b/static/scripts/packed/galaxy.panels.js Thu Jan 07 15:45:15 2010 -0500 @@ -1,1 +1,1 @@ -function ensure_dd_helper(){if($("#DD-helper").length==0){$("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_left_panel(h,c,e){var g=false;var f=null;var d=function(i){var j=i;if(i<0){i=0}$(h).css("width",i);$(e).css("left",j);$(c).css("left",i+7);if(document.recalc){document.recalc()}};var 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);m.append(c);return c}});var FeatureTrack=function(c,b,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b== "pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{track_type:b.track_type,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:functi on(a,b){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get _data(G,c);return}h=this.incremental_slots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}va r I=m.blocks;if(I){if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}}); \ No newline at end of file +var DEBUG=false;var DENSITY=1000,FEATURE_LEVELS=100,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=20,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="../images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="../images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="../images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="../images/visualization/strand_left_inv.png";left_ img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.obj_cache={};this.key_ary=[]};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c}});var View=function(b,a){this.chrom=b;this.tracks=[];this.max_low=0;this.max_high=a;this.center=(this.max_high-this.max_low)/2;this.span=this.max_high-this.max_low;this.zoom_factor=3;this.zoom_level=0};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=thi s.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/DENSITY)/Math.LN10));this.zoom_res=Math.max(1,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS)));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));for(var c=0,a=this.tracks.length;c<a;c++){this.tracks[c].draw()}},zoom_in:function(a){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/$(document).width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;thi s.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var l=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(l);var m=this.content_div.width()/f;var i=20;var h;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_off set){b-=this.left_offset}c.css({left:b});l.append(c);i=Math.max(i,c.height())}else{h=this.draw_tile(d,a,l,m);if(h){this.tile_cache.set(k,h);i=Math.max(i,h.height())}}this.content_div.css("height",i);a+=1}}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_LINE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("line -track");this.dataset_id=b;this.data_queue={};this.cache=new Cache(CACHED_DATA)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{stats:true,indexer:a.indexer,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){if(!c||c=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(c=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(c=="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.min_value=c.min;a.max_value=c.max;a.vertical_range=a.max_value-a.min_value;var d=$("<div class='yaxislabel'>"+a.min_value+"</div>");var b=$("<div class='yaxislabel'>"+a.max_value+"</div>");b.css({position:"relative",top:"35px"});b.prependTo(a.container_div);d.css({position:"relative",top:a.height_ px+32+"px"});d.prependTo(a.container_div);a.draw()}}}})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.getJSON(data_url,{indexer:this.indexer,chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},function(g){c.cache.set(e,g);delete c.data_queue[e];c.draw()})}},draw_tile:function(d,a,m,o){if(!this.vertical_range){return}var h=a*DENSITY*d,b=DENSITY*d,c=$("<canvas class='tile'></canvas>"),l=d+"_"+a;if(!this.cache.get(l)){this.get_data(d,a);return}var g=this.cache.get(l);c.css({position:"absolute",top:0,left:(h-this.view.low)*o});c.get(0).width=Math.ceil(b*o);c.get(0).height=this.height_px;var n=c.get(0).getContext("2d");var e=false;n.beginPath();for(var f=0;f<g.length-1;f++){var k=g[f][0]-h;var j=g[f][1];if(isNaN(j)){e=false}else{k=k*o;j=(j-this.min_value)/this.vertical_range*this.height_px;if(e){n.lineTo(k,j)}else{n.moveTo(k,j);e=true}}}n.stroke();m.append(c);retu rn c}});var FeatureTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.indexer=d;this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.001;this.showing_labels=false;this.vertical_gap=10;this.base_color="#2C3143";this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.data_cache=new Cache(20)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;a.content_div.text(DATA_LOADING);$.getJSON(data_url,{indexer:a.indexer,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(b.length===0||b=="no data"){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b=="pending"){a.container_div.addCla ss("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}}})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{indexer:b.indexer,chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,include_blocks:true},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},calc_slots:function(){var c=[],b=this.content_div.width()/(this.view.high-this.view.low),a=this.view.max_high,e=this.view.max_low;for(var f=0,g=this.values.length;f<g;f++){var h,k,l=this.values[f];h=Math.floor((l.start-e)*b);k=Math.ceil((l.end-e)*b);var d=0;while(true){if(c[d]===undefined||c[d]<h){c[d]=k;this.zo_slots[l.uid]=d;break}d++}}this.height_px=c.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},incremental_slots:function(a,b){if(!this.inc_slots[a]){this.inc _slots[a]={};this.inc_slots[a].w_scale=DENSITY/Math.pow(FEATURE_LEVELS,a+1)}var k=this.inc_slots[a];var d=[],l=[],c=0,m=$("<canvas></canvas>").get(0).getContext("2d"),f=this.view.max_low;for(var g=0,h=b.length;g<h;g++){var n=b[g];if(k[n.uid]){c=Math.max(c,k[n.uid]);d[k[n.uid]]=Math.ceil((n.end-f)*k.w_scale)}else{l.push(n)}}for(var g=0,h=l.length;g<h;g++){var n=l[g];f_start=Math.floor((n.start-f)*k.w_scale);f_start-=m.measureText(n.name).width;f_end=Math.ceil((n.end-f)*k.w_scale);var e=0;while(true){if(d[e]===undefined||d[e]<f_start){d[e]=f_end;k[n.uid]=e;c=Math.max(c,e);break}e++}}return c},draw_tile:function(A,F,n,r){if(!this.values){return}var G=F*DENSITY*A,c=(F+1)*DENSITY*A,v=DENSITY*A;var K,u,h;if(r>this.show_labels_scale){if(!this.showing_labels){this.showing_labels=true}for(var B in this.data_cache.obj_cache){var p=B.split("_"),e=p[0],d=p[1];if(e<=G&&d>=c){K=this.data_cache.get(B);break}}if(!K){this.data_queue[[G,c]]=true;this.get_data(G,c);return}h=this.incremental_sl ots(this.view.zoom_res,K)*this.vertical_gap+15;u=this.inc_slots[this.view.zoom_res]}else{if(this.showing_labels){this.showing_labels=false}h=this.height_px;u=this.zo_slots;K=this.values}var y=Math.ceil(v*r),x=$("<canvas class='tile'></canvas>");x.css({position:"absolute",top:0,left:(G-this.view.low)*r-this.left_offset});x.get(0).width=y+this.left_offset;x.get(0).height=h;var z=x.get(0).getContext("2d");z.fillStyle=this.base_color;z.font=this.default_font;z.textAlign="right";var C=0;for(var D=0,E=K.length;D<E;D++){var m=K[D];if(m.start<=c&&m.end>=G){var g=Math.floor(Math.max(0,(m.start-G)*r)),l=Math.ceil(Math.min(y,(m.end-G)*r)),f=u[m.uid]*this.vertical_gap;var a,L,b=null,s=null;if(m.thick_start&&m.thick_end){b=Math.floor(Math.max(0,(m.thick_start-G)*r));s=Math.ceil(Math.min(y,(m.thick_end-G)*r))}if(!this.showing_labels){z.fillRect(g+this.left_offset,f+5,l-g,1)}else{if(z.fillText&&m.start>G){z.fillText(m.name,g-1+this.left_offset,f+8)}var I=m.blocks;if(I){if(m.strand){if(m.st rand=="+"){z.fillStyle=RIGHT_STRAND}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}for(var B=0,J=I.length;B<J;B++){var q=I[B],o=Math.floor(Math.max(0,(q[0]-G)*r)),H=Math.ceil(Math.min(y,(q[1]-G)*r));if(o>H){continue}a=5;L=3;z.fillRect(o+this.left_offset,f+L,H-o,a);if(b&&(o<s||H>b)){a=9;L=1;var w=Math.max(o,b),t=Math.min(H,s);z.fillRect(w+this.left_offset,f+L,t-w,a)}}}else{a=9;L=1;z.fillRect(g+this.left_offset,f+L,l-g,a);if(m.strand){if(m.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(m.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(g+this.left_offset,f,l-g,10);z.fillStyle=this.base_color}}}C++}}n.append(x);return x}});var ReadTrack=function(c,b,d,a){this.tile_cache=new Cache(CACHED_TILES_FEATURE);Track.call(this,c,$("#viewport"));TiledTrack.call(this);FeatureTrack.call(this,c,b,d,a);this.default_font="9px Monaco, Lucida Console, monospace"};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureT rack.prototype,{draw_tile:function(w,A,n,o){if(!this.values){return}var B=A*DENSITY*w,f=(A+1)*DENSITY*w,r=DENSITY*w;var E,q,k;k=this.height_px;q=this.zo_slots;E=this.values;var u=Math.ceil(r*o),s=$("<canvas class='tile'></canvas>");var b=$("<canvas></canvas>").get(0).getContext("2d");s.css({position:"absolute",top:0,left:(B-this.view.low)*o-this.left_offset});s.get(0).width=u+this.left_offset;s.get(0).height=k;var v=s.get(0).getContext("2d");v.fillStyle=this.base_color;v.font=this.default_font;v.textAlign="right";var t=v.measureText("A").width;var x=0;for(var y=0,z=E.length;y<z;y++){var m=E[y];if(m.start<=f&&m.end>=B){var h=Math.floor(Math.max(0,(m.start-B)*o)),l=Math.ceil(Math.min(u,(m.end-B)*o)),g=q[m.uid]*this.vertical_gap;var a,F,e=null,p=null;if(o>t){for(var C=0,d=m.name.length;C<d;C++){var D=Math.floor(Math.max(0,(m.start+C-B)*o));v.fillText(m.name[C],D+this.left_offset,g+8)}}else{v.fillRect(h+this.left_offset,g+4,l-h,3)}}}n.append(s);return s}}); \ No newline at end of file diff -r 427d93bf3d39 -r 7d3667e8e415 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Jan 07 14:52:51 2010 -0500 +++ b/static/scripts/trackster.js Thu Jan 07 15:45:15 2010 -0500 @@ -81,7 +81,7 @@ this.max_high = max_high; this.center = (this.max_high - this.max_low) / 2; this.span = this.max_high - this.max_low; - this.zoom_factor = 2; + this.zoom_factor = 3; this.zoom_level = 0; }; $.extend( View.prototype, { @@ -241,12 +241,12 @@ } }); -var LineTrack = function ( name, dataset_id, height ) { +var LineTrack = function ( name, dataset_id, indexer, height ) { this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); - this.track_type = "line"; + this.indexer = indexer; this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; @@ -258,7 +258,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); - $.getJSON( data_url, { stats: true, track_type: track.track_type, + $.getJSON( data_url, { stats: true, indexer: track.indexer, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { if (!data || data == "error") { @@ -300,7 +300,7 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, + $.getJSON( data_url, { indexer: this.indexer, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id, resolution: this.view.resolution }, function ( data ) { track.cache.set(key, data); @@ -360,12 +360,12 @@ } }); -var FeatureTrack = function ( name, dataset_id, height ) { +var FeatureTrack = function ( name, dataset_id, indexer, height ) { this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); - this.track_type = "feature"; + this.indexer = indexer; this.height_px = (height ? height : 100); this.container_div.addClass( "feature-track" ); this.dataset_id = dataset_id; @@ -384,7 +384,7 @@ init: function() { var track = this; track.content_div.text(DATA_LOADING); - $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, + $.getJSON( data_url, { indexer: track.indexer, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { if (data == "error") { @@ -414,7 +414,7 @@ if (!track.data_queue[key]) { track.data_queue[key] = true; - $.getJSON( data_url, { track_type: track.track_type, chrom: track.view.chrom, + $.getJSON( data_url, { indexer: track.indexer, chrom: track.view.chrom, low: low, high: high, dataset_id: track.dataset_id, include_blocks: true }, function ( data ) { track.data_cache.set(key, data); @@ -454,8 +454,6 @@ if (!this.inc_slots[level]) { this.inc_slots[level] = {}; this.inc_slots[level].w_scale = DENSITY / Math.pow(FEATURE_LEVELS, level+1); - // this.inc_slots[level].w_scale = 1000 / (this.view.high - this.view.low); - } var slots = this.inc_slots[level]; // console.log(level, slots.w_scale, slots); @@ -629,3 +627,71 @@ return new_canvas; } }); + +var ReadTrack = function ( name, dataset_id, indexer, height ) { + this.tile_cache = new Cache(CACHED_TILES_FEATURE); + Track.call( this, name, $("#viewport") ); + TiledTrack.call( this ); + FeatureTrack.call( this, name, dataset_id, indexer, height ); + this.default_font = "9px Monaco, Lucida Console, monospace"; + +}; +$.extend( ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { + draw_tile: function( resolution, tile_index, parent_element, w_scale ) { + if (!this.values) { + return; + } + var tile_low = tile_index * DENSITY * resolution, + tile_high = ( tile_index + 1 ) * DENSITY * resolution, + tile_span = DENSITY * resolution; + // console.log("drawing " + tile_index); + // Once we zoom in enough, show name labels + var data, slots, required_height; + required_height = this.height_px; + slots = this.zo_slots; + data = this.values; + + // console.log(tile_low, tile_high, tile_length, w_scale); + var width = Math.ceil( tile_span * w_scale ), + new_canvas = $("<canvas class='tile'></canvas>"); + + var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); + + new_canvas.css({ + position: "absolute", + top: 0, + left: ( tile_low - this.view.low ) * w_scale - this.left_offset + }); + new_canvas.get(0).width = width + this.left_offset; + new_canvas.get(0).height = required_height; + // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); + var ctx = new_canvas.get(0).getContext("2d"); + ctx.fillStyle = this.base_color; + ctx.font = this.default_font; + ctx.textAlign = "right"; + var px_per_char = ctx.measureText("A").width; + + var j = 0; + for (var i = 0, len = data.length; i < len; i++) { + var feature = data[i]; + if (feature.start <= tile_high && feature.end >= tile_low) { + var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), + f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), + y_center = slots[feature.uid] * this.vertical_gap; + + var thickness, y_start, thick_start = null, thick_end = null; + if (w_scale > px_per_char) { + for (var c = 0, str_len = feature.name.length; c < str_len; c++) { + var c_start = Math.floor( Math.max(0, (feature.start + c - tile_low) * w_scale) ); + ctx.fillText(feature.name[c], c_start + this.left_offset, y_center + 8); + } + } else { + ctx.fillRect(f_start + this.left_offset, y_center + 4, f_end - f_start, 3); + } + } + } + + parent_element.append( new_canvas ); + return new_canvas; + } +}); diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu Jan 07 14:52:51 2010 -0500 +++ b/templates/tracks/browser.mako Thu Jan 07 15:45:15 2010 -0500 @@ -20,7 +20,7 @@ view.add_track( new LabelTrack( $("#nav-labeltrack" ) ) ); %for track in tracks: - view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']} ) ); + view.add_track( new ${track["type"]}( "${track['name']}", ${track['dataset_id']}, "${track['indexer']}" ) ); %endfor $(document).bind( "redraw", function( e ) { diff -r 427d93bf3d39 -r 7d3667e8e415 templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Thu Jan 07 14:52:51 2010 -0500 +++ b/templates/tracks/new_browser.mako Thu Jan 07 15:45:15 2010 -0500 @@ -11,7 +11,7 @@ </script> </%def> -% if not converters: +% if not available_tracks: <div class="errormessagelarge"> There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains converters for datatypes (see tool_conf.xml.sample) for examples. @@ -46,7 +46,7 @@ <div style="clear: both;"></div> </div> <div class="form-row"> - <label for="dataset_ids">Datasets to include: </label> + <label for="dataset_ids">Datasets to visualize: (${", ".join(available_tracks)} files are supported)</label> %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): <div> <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" />

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