1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/606085ebe5f5/ changeset: 606085ebe5f5 user: kanwei date: 2011-08-24 22:43:02 summary: sam2interval: Add read_name column affected #: 4 files (18.4 KB) --- a/test-data/sam2interval_noprintAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_noprintAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,7 +1,7 @@ -#chrom start end strand -ref 6 22 + -ref 8 19 + -ref 8 14 + -ref 15 40 + -ref 28 33 - -ref 36 45 - +#chrom start end strand read_name +ref 6 22 + r001 +ref 8 19 + r002 +ref 8 14 + r003 +ref 15 40 + r004 +ref 28 33 - r003 +ref 36 45 - r001 --- a/test-data/sam2interval_printAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_printAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,4 +1,4 @@ -#chrom start end strand +#chrom start end strand read_name ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 --- a/test-data/sam2interval_with_unmapped_reads_noprintAll.dat Wed Aug 24 15:33:07 2011 -0400 +++ b/test-data/sam2interval_with_unmapped_reads_noprintAll.dat Wed Aug 24 16:43:02 2011 -0400 @@ -1,927 +1,927 @@ -#chrom start end strand -chrM 6565 6641 - 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-chrM 2462 2538 - -chrM 8469 8545 + -chrM 11092 11168 - -chrM 6473 6549 + -chrM 16220 16296 - -chrM 4832 4908 + -chr17 22023725 22023801 - -chr1 567374 567450 - -chrM 11821 11897 + -chrM 8061 8137 - -chr5 134260199 134260275 - -chrM 9877 9953 - -chrM 11833 11909 + -chrM 3658 3734 - -chrM 861 937 - -chrM 5607 5683 + -chrM 8622 8698 - -chrM 9468 9544 + -chrM 10362 10438 - -chrM 3138 3214 + -chrM 4320 4396 - -chr1 567521 567597 - -chrM 8468 8544 + -chrM 3891 3967 - -chrM 13657 13733 - -chrM 9922 9998 - -chrM 15865 15941 + -chrM 5353 5429 - -chrM 8744 8820 + -chrM 5339 5415 + -chrM 3734 3810 + -chrM 4252 4328 + -chrM 13502 13578 + -chrM 16346 16422 + +#chrom start end strand read_name +chrM 6565 6641 - GA5:3:1:24:1745#0/1 +chrM 4096 4172 - GA5:3:1:23:263#0/1 +chrM 14759 14835 - GA5:3:1:24:1658#0/1 +chrM 1244 1320 - GA5:3:1:24:1108#0/1 +chrM 5317 5393 + GA5:3:1:24:1272#0/1 +chrM 10934 11010 - GA5:3:1:25:1989#0/1 +chr1 567534 567610 - GA5:3:1:25:1877#0/1 +chrM 16407 16483 - GA5:3:1:25:1203#0/1 +chrM 8684 8760 + GA5:3:1:24:1720#0/1 +chrM 4952 5028 - GA5:3:1:25:74#0/1 +chr1 567927 568003 - GA5:3:1:26:129#0/1 +chrM 6830 6906 - GA5:3:1:27:1860#0/1 +chrM 7432 7508 + GA5:3:1:26:303#0/1 +chrM 5342 5418 - GA5:3:1:27:509#0/1 +chrM 3199 3275 - GA5:3:1:27:1876#0/1 +chrM 1392 1468 + GA5:3:1:27:462#0/1 +chrM 7909 7985 + GA5:3:1:27:1826#0/1 +chr2 49456941 49457017 - GA5:3:1:28:1961#0/1 +chrM 16239 16315 + GA5:3:1:25:1902#0/1 +chrM 11515 11591 - GA5:3:1:28:704#0/1 +chrM 7343 7419 - GA5:3:1:29:78#0/1 +chrM 5628 5704 + GA5:3:1:29:65#0/1 +chrM 9238 9314 + GA5:3:1:30:571#0/1 +chrM 202 278 - GA5:3:1:30:1418#0/1 +chrM 10065 10141 + GA5:3:1:31:1998#0/1 +chrM 9875 9951 + GA5:3:1:32:1159#0/1 +chrM 9031 9107 - GA5:3:1:32:1723#0/1 +chr1 564778 564854 - GA5:3:1:32:1365#0/1 +chrM 5333 5409 - GA5:3:1:33:300#0/1 +chrM 435 511 + GA5:3:1:33:625#0/1 +chrM 4066 4142 + GA5:3:1:33:1597#0/1 +chrM 6214 6290 + GA5:3:1:32:1051#0/1 +chrM 7217 7293 - GA5:3:1:33:1476#0/1 +chrM 11261 11337 - GA5:3:1:34:1493#0/1 +chrM 14521 14597 - GA5:3:1:35:718#0/1 +chrM 3593 3669 - GA5:3:1:35:1074#0/1 +chr17 22023720 22023796 - GA5:3:1:35:1946#0/1 +chrM 12846 12922 - GA5:3:1:36:143#0/1 +chrM 7047 7123 - GA5:3:1:38:1282#0/1 +chrM 2693 2769 + GA5:3:1:36:258#0/1 +chrM 8062 8138 - GA5:3:1:38:1622#0/1 +chrM 6159 6235 + GA5:3:1:39:651#0/1 +chr1 566417 566493 - GA5:3:1:40:1756#0/1 +chrM 3031 3107 - GA5:3:1:41:277#0/1 +chrM 6276 6352 + GA5:3:1:41:24#0/1 +chrM 14786 14862 - GA5:3:1:42:1739#0/1 +chrM 10589 10665 + GA5:3:1:44:1997#0/1 +chrM 16248 16324 - GA5:3:1:42:449#0/1 +chrM 7319 7395 + GA5:3:1:44:1202#0/1 +chrM 3527 3603 + GA5:3:1:44:1689#0/1 +chrM 13998 14074 + GA5:3:1:45:1004#0/1 +chrM 13229 13305 + GA5:3:1:46:1996#0/1 +chrM 7456 7532 - GA5:3:1:46:1624#0/1 +chrM 5109 5185 - GA5:3:1:47:148#0/1 +chrM 2909 2985 + GA5:3:1:46:1928#0/1 +chr13 110076579 110076655 + GA5:3:1:48:345#0/1 +chr1 566432 566508 - GA5:3:1:49:208#0/1 +chr1 565743 565819 - GA5:3:1:48:1620#0/1 +chrM 3155 3231 - GA5:3:1:48:1536#0/1 +chrM 4657 4733 + GA5:3:1:49:1377#0/1 +chrM 7368 7444 + GA5:3:1:51:1072#0/1 +chrM 5329 5405 - GA5:3:1:51:78#0/1 +chrM 2171 2247 - GA5:3:1:51:851#0/1 +chr1 568282 568358 + GA5:3:1:52:518#0/1 +chrM 4376 4452 + GA5:3:1:52:796#0/1 +chrM 14645 14721 - GA5:3:1:52:192#0/1 +chrM 4694 4770 - GA5:3:1:55:1412#0/1 +chrM 2412 2488 + GA5:3:1:53:1458#0/1 +chrM 9057 9133 - GA5:3:1:55:1305#0/1 +chrM 10527 10603 + GA5:3:1:55:855#0/1 +chr1 564493 564569 - GA5:3:1:55:451#0/1 +chrM 7102 7178 + GA5:3:1:55:299#0/1 +chrM 10896 10972 - GA5:3:1:55:1194#0/1 +chrM 13626 13702 + GA5:3:1:56:1499#0/1 +chrM 5609 5685 + GA5:3:1:57:959#0/1 +chrM 7666 7742 - GA5:3:1:56:473#0/1 +chrM 14730 14806 + GA5:3:1:56:636#0/1 +chrM 10682 10758 + GA5:3:1:57:1408#0/1 +chrM 5069 5145 + GA5:3:1:58:763#0/1 +chr1 566474 566550 - GA5:3:1:59:688#0/1 +chrM 9140 9216 + GA5:3:1:59:791#0/1 +chrM 16340 16416 - GA5:3:1:59:503#0/1 +chr1 565718 565794 - GA5:3:1:61:1190#0/1 +chrM 6732 6808 + GA5:3:1:58:1920#0/1 +chrM 16239 16315 + GA5:3:1:57:1111#0/1 +chrM 3180 3256 - GA5:3:1:61:1838#0/1 +chrM 13789 13865 + GA5:3:1:61:722#0/1 +chrM 10350 10426 + GA5:3:1:62:1796#0/1 +chrM 10519 10595 - GA5:3:1:62:1469#0/1 +chrM 5391 5467 + GA5:3:1:63:1214#0/1 +chrM 6420 6496 - GA5:3:1:61:594#0/1 +chrM 745 821 - GA5:3:1:62:1922#0/1 +chrM 1023 1099 + GA5:3:1:63:762#0/1 +chr1 569720 569796 + GA5:3:1:61:900#0/1 +chr1 569272 569348 + GA5:3:1:63:462#0/1 +chrM 10091 10167 + GA5:3:1:63:709#0/1 +chrM 10937 11013 - GA5:3:1:63:1686#0/1 +chrM 6460 6536 - GA5:3:1:64:1185#0/1 +chrM 12342 12418 + GA5:3:1:64:1804#0/1 +chrM 8694 8770 - GA5:3:1:67:480#0/1 +chrM 2104 2180 + GA5:3:1:65:500#0/1 +chrM 16386 16462 - GA5:3:1:68:398#0/1 +chrM 3224 3300 + GA5:3:1:67:298#0/1 +chr1 564901 564977 - GA5:3:1:67:612#0/1 +chr1 564729 564805 - GA5:3:1:68:336#0/1 +chrM 6453 6529 - GA5:3:1:68:1266#0/1 +chrM 9602 9678 - GA5:3:1:68:1282#0/1 +chrM 5756 5832 + GA5:3:1:72:332#0/1 +chrM 10562 10638 + GA5:3:1:72:1394#0/1 +chrM 2816 2892 + GA5:3:1:69:117#0/1 +chrM 9681 9757 - GA5:3:1:72:1576#0/1 +chrM 11237 11313 - GA5:3:1:72:1817#0/1 +chrM 3920 3996 - GA5:3:1:72:1884#0/1 +chrM 8192 8268 + GA5:3:1:73:1128#0/1 +chrM 1720 1796 - GA5:3:1:73:1334#0/1 +chrM 14707 14783 - GA5:3:1:73:870#0/1 +chrM 11125 11201 - GA5:3:1:73:743#0/1 +chr1 569107 569183 + GA5:3:1:73:124#0/1 +chrM 9111 9187 + GA5:3:1:73:1774#0/1 +chrM 3908 3984 + GA5:3:1:74:276#0/1 +chrM 14018 14094 - GA5:3:1:74:1707#0/1 +chrM 11284 11360 - GA5:3:1:75:739#0/1 +chrM 3592 3668 - GA5:3:1:75:1808#0/1 +chrM 14471 14547 + GA5:3:1:75:1740#0/1 +chrM 2865 2941 - GA5:3:1:76:1071#0/1 +chrM 9703 9779 + GA5:3:1:78:1517#0/1 +chrM 16034 16110 - GA5:3:1:77:509#0/1 +chr5 134262582 134262658 - GA5:3:1:77:84#0/1 +chrM 2197 2273 - GA5:3:1:77:137#0/1 +chrM 15072 15148 - GA5:3:1:79:1703#0/1 +chrM 13030 13106 - GA5:3:1:78:1438#0/1 +chrM 12457 12533 - GA5:3:1:80:1988#0/1 +chrM 1868 1944 - GA5:3:1:79:708#0/1 +chrM 10249 10325 + GA5:3:1:81:1195#0/1 +chrM 12210 12286 + GA5:3:1:82:274#0/1 +chrM 4022 4098 - GA5:3:1:82:806#0/1 +chrM 16199 16275 + GA5:3:1:83:1274#0/1 +chrM 13120 13196 - GA5:3:1:83:13#0/1 +chrM 13023 13099 - GA5:3:1:83:466#0/1 +chrM 8719 8795 - GA5:3:1:82:161#0/1 +chrM 8674 8750 - GA5:3:1:84:1918#0/1 +chr1 569410 569486 - GA5:3:1:86:1188#0/1 +chrM 16066 16142 - GA5:3:1:85:383#0/1 +chr11 10529687 10529763 - GA5:3:1:85:419#0/1 +chrM 7208 7284 - GA5:3:1:86:1840#0/1 +chrM 10193 10269 + GA5:3:1:86:1396#0/1 +chrM 1280 1356 - GA5:3:1:86:1670#0/1 +chrM 14135 14211 - GA5:3:1:87:1553#0/1 +chrM 131 207 - GA5:3:1:87:968#0/1 +chrM 847 923 - GA5:3:1:88:944#0/1 +chrM 8651 8727 - GA5:3:1:88:722#0/1 +chrM 14879 14955 + GA5:3:1:88:1905#0/1 +chrM 15558 15634 - GA5:3:1:90:183#0/1 +chrM 2986 3062 - GA5:3:1:91:1288#0/1 +chrM 2502 2578 + GA5:3:1:91:1865#0/1 +chrM 9781 9857 - GA5:3:1:93:1339#0/1 +chrM 13380 13456 - GA5:3:1:93:289#0/1 +chr3 96335987 96336063 - GA5:3:1:91:1901#0/1 +chrM 7094 7170 - GA5:3:1:93:31#0/1 +chrM 15731 15807 - GA5:3:1:93:607#0/1 +chrM 12004 12080 + GA5:3:1:90:1958#0/1 +chrM 12835 12911 + GA5:3:1:93:1806#0/1 +chrM 3314 3390 - GA5:3:1:94:1167#0/1 +chrM 4030 4106 + GA5:3:1:94:636#0/1 +chr1 569884 569960 - GA5:3:1:93:1176#0/1 +chrM 6647 6723 + GA5:3:1:94:131#0/1 +chr1 566600 566676 - GA5:3:1:95:952#0/1 +chrM 2430 2506 + GA5:3:1:94:989#0/1 +chrM 12833 12909 + GA5:3:1:94:703#0/1 +chr1 568256 568332 + GA5:3:1:95:1072#0/1 +chrM 13222 13298 - GA5:3:1:95:866#0/1 +chrM 10321 10397 - GA5:3:1:96:1665#0/1 +chrM 8614 8690 - GA5:3:1:96:1702#0/1 +chrM 6581 6657 + GA5:3:1:97:734#0/1 +chrM 3526 3602 + GA5:3:1:97:239#0/1 +chrM 11413 11489 + GA5:3:1:98:1829#0/1 +chrM 9826 9902 - GA5:3:1:98:1819#0/1 +chr5 134259175 134259251 - GA5:3:1:98:222#0/1 +chrM 3314 3390 - GA5:3:1:99:476#0/1 +chrM 11146 11222 - GA5:3:1:98:271#0/1 +chrM 2735 2811 + GA5:3:1:98:770#0/1 +chrM 1695 1771 + GA5:3:1:100:1425#0/1 +chrM 3333 3409 - GA5:3:1:99:1469#0/1 +chr1 567391 567467 - GA5:3:1:100:1178#0/1 +chrM 3110 3186 - GA5:3:1:101:849#0/1 +chr1 567574 567650 - GA5:3:1:102:707#0/1 +chrM 15552 15628 + GA5:3:1:103:1995#0/1 +chrX 125606487 125606563 - GA5:3:1:99:740#0/1 +chrM 9205 9281 + GA5:3:1:103:300#0/1 +chr5 134260176 134260252 - GA5:3:1:103:505#0/1 +chrM 3023 3099 - GA5:3:1:103:1266#0/1 +chr1 566110 566186 + GA5:3:1:103:637#0/1 +chr1 569285 569361 - GA5:3:1:104:856#0/1 +chrM 12692 12768 + GA5:3:1:100:1609#0/1 +chrM 10442 10518 + GA5:3:1:104:645#0/1 +chrM 8008 8084 + GA5:3:1:104:948#0/1 +chr1 567269 567345 + GA5:3:1:105:775#0/1 +chrM 10796 10872 + GA5:3:1:104:1070#0/1 +chrM 2903 2979 - GA5:3:1:104:1800#0/1 +chrM 10349 10425 + GA5:3:1:106:1608#0/1 +chr13 110076645 110076721 - GA5:3:1:108:1351#0/1 +chrM 9283 9359 - GA5:3:1:107:1114#0/1 +chrM 2816 2892 + GA5:3:1:108:1305#0/1 +chrM 2816 2892 + GA5:3:1:108:615#0/1 +chrM 6529 6605 + GA5:3:1:110:954#0/1 +chrM 16312 16388 - GA5:3:1:111:941#0/1 +chrM 5295 5371 + GA5:3:1:111:207#0/1 +chrM 4061 4137 - GA5:3:1:112:1363#0/1 +chrM 5949 6025 + GA5:3:1:112:974#0/1 +chrM 2680 2756 - GA5:3:1:113:519#0/1 +chrM 4032 4108 + GA5:3:1:112:1748#0/1 +chrM 13081 13157 + GA5:3:1:113:728#0/1 +chrM 2979 3055 - GA5:3:1:113:1888#0/1 +chrM 2335 2411 + GA5:3:1:113:1937#0/1 +chr1 567560 567636 + GA5:3:1:114:1152#0/1 +chrM 14790 14866 + GA5:3:1:114:1895#0/1 +chrM 1316 1392 - GA5:3:1:114:910#0/1 +chr1 568495 568571 - GA5:3:1:114:1273#0/1 +chrM 15907 15983 + GA5:3:1:115:1736#0/1 +chrM 3937 4013 + GA5:3:1:116:1034#0/1 +chrM 2357 2433 + GA5:3:1:116:1207#0/1 +chr1 567258 567334 + GA5:3:1:115:454#0/1 +chrM 10600 10676 - GA5:3:1:116:898#0/1 +chrM 8474 8550 - GA5:3:1:116:1215#0/1 +chrM 11515 11591 - GA5:3:1:117:1182#0/1 +chr1 567287 567363 + GA5:3:1:117:422#0/1 +chrM 11167 11243 + GA5:3:1:118:1611#0/1 +chrM 15521 15597 - GA5:3:1:117:643#0/1 +chrM 10943 11019 - GA5:3:1:118:598#0/1 +chrM 6201 6277 + GA5:3:1:118:1255#0/1 +chrM 12696 12772 - GA5:3:1:120:134#0/1 +chrM 10796 10872 + GA5:3:1:119:783#0/1 +chrM 2960 3036 - GA5:3:1:120:1597#0/1 +chrM 14774 14850 + GA5:3:1:120:122#0/1 +chrM 9545 9621 + GA5:3:1:121:1197#0/1 +chrM 1007 1083 - GA5:3:1:121:1070#0/1 +chrM 14806 14882 - GA5:3:1:121:277#0/1 +chrM 14909 14985 - GA5:3:1:122:604#0/1 +chrM 9123 9199 + GA5:3:1:123:334#0/1 +chrM 7198 7274 - GA5:3:1:123:1597#0/1 +chr1 568855 568931 - GA5:3:1:122:153#0/1 +chrM 11186 11262 - GA5:3:1:123:1737#0/1 +chrM 1094 1170 + GA5:3:1:125:126#0/1 +chrM 1754 1830 + GA5:3:1:125:1359#0/1 +chrM 6393 6469 + GA5:3:1:126:1749#0/1 +chrM 8906 8982 - GA5:3:1:126:102#0/1 +chrM 3919 3995 - GA5:3:1:127:288#0/1 +chrM 10951 11027 + GA5:3:1:126:1454#0/1 +chrM 6624 6700 - GA5:3:1:127:711#0/1 +chrM 7883 7959 + GA5:3:1:130:1391#0/1 +chr1 567275 567351 + GA5:3:1:129:1716#0/1 +chrM 6483 6559 + GA5:3:1:131:1895#0/1 +chrM 9937 10013 - GA5:3:1:132:1632#0/1 +chrM 6529 6605 - GA5:3:1:132:1866#0/1 +chrM 3650 3726 - GA5:3:1:131:1555#0/1 +chrM 10905 10981 - GA5:3:1:133:152#0/1 +chrM 8023 8099 + GA5:3:1:133:261#0/1 +chrM 10902 10978 + GA5:3:1:133:884#0/1 +chrM 6461 6537 + GA5:3:1:133:793#0/1 +chrM 13049 13125 - GA5:3:1:134:409#0/1 +chrM 11515 11591 - GA5:3:1:134:937#0/1 +chrM 5360 5436 - GA5:3:1:135:4#0/1 +chrM 11605 11681 + GA5:3:1:136:764#0/1 +chrM 2357 2433 - GA5:3:1:136:1126#0/1 +chrM 6309 6385 + GA5:3:1:137:774#0/1 +chr1 567281 567357 + GA5:3:1:136:1459#0/1 +chr7 45291595 45291671 - GA5:3:1:137:385#0/1 +chrM 14614 14690 - GA5:3:1:138:1810#0/1 +chrM 2978 3054 - GA5:3:1:138:422#0/1 +chrM 7048 7124 - GA5:3:1:138:1360#0/1 +chrM 11084 11160 - GA5:3:1:139:124#0/1 +chrM 2259 2335 - GA5:3:1:139:1525#0/1 +chrM 5416 5492 - GA5:3:1:140:1536#0/1 +chr5 134263614 134263690 - GA5:3:1:140:1015#0/1 +chrM 14179 14255 - GA5:3:1:140:1072#0/1 +chr1 566599 566675 + GA5:3:1:141:9#0/1 +chrM 14895 14971 - GA5:3:1:141:734#0/1 +chr13 110076472 110076548 + GA5:3:1:141:473#0/1 +chrM 7849 7925 - GA5:3:1:141:1890#0/1 +chrM 14822 14898 + GA5:3:1:143:1226#0/1 +chr1 569878 569954 + GA5:3:1:142:635#0/1 +chrM 3272 3348 - GA5:3:1:141:548#0/1 +chrM 12276 12352 - GA5:3:1:143:1775#0/1 +chrM 5839 5915 + GA5:3:1:144:603#0/1 +chrM 9009 9085 + GA5:3:1:143:1215#0/1 +chr1 569321 569397 - GA5:3:1:145:350#0/1 +chrM 11416 11492 - GA5:3:1:145:644#0/1 +chrM 3866 3942 - GA5:3:1:146:75#0/1 +chrM 11415 11491 - GA5:3:1:145:1743#0/1 +chrM 9583 9659 - GA5:3:1:146:229#0/1 +chrM 10422 10498 - GA5:3:1:146:1848#0/1 +chrM 9066 9142 + GA5:3:1:147:11#0/1 +chrM 11515 11591 - GA5:3:1:147:148#0/1 +chrM 15452 15528 + GA5:3:1:148:1088#0/1 +chrM 239 315 + GA5:3:1:147:1796#0/1 +chrM 16322 16398 + GA5:3:1:148:200#0/1 +chrM 1012 1088 - GA5:3:1:149:607#0/1 +chrM 6176 6252 - GA5:3:1:150:1681#0/1 +chrM 10809 10885 + GA5:3:1:145:528#0/1 +chr1 568094 568170 - GA5:3:1:151:1905#0/1 +chrM 13321 13397 - GA5:3:1:152:1759#0/1 +chrM 5752 5828 - GA5:3:1:151:117#0/1 +chrM 4132 4208 + GA5:3:1:152:348#0/1 +chrM 16250 16326 - GA5:3:1:150:1406#0/1 +chrM 10796 10872 + GA5:3:1:153:1969#0/1 +chrM 11898 11974 - GA5:3:1:155:1916#0/1 +chr1 564877 564953 + GA5:3:1:154:190#0/1 +chrM 8256 8332 + GA5:3:1:155:1870#0/1 +chrM 15488 15564 + GA5:3:1:156:1707#0/1 +chrM 2804 2880 + GA5:3:1:157:280#0/1 +chrM 4878 4954 + GA5:3:1:156:977#0/1 +chrM 11258 11334 - GA5:3:1:157:1848#0/1 +chrM 4153 4229 + GA5:3:1:158:172#0/1 +chrM 11225 11301 - GA5:3:1:158:451#0/1 +chrM 892 968 - GA5:3:1:159:1719#0/1 +chrM 4399 4475 - GA5:3:1:158:1248#0/1 +chr18 45379660 45379736 - GA5:3:1:158:147#0/1 +chrM 9171 9247 - GA5:3:1:160:1547#0/1 +chrM 3176 3252 + GA5:3:1:160:687#0/1 +chrM 1013 1089 - GA5:3:1:161:170#0/1 +chrM 6704 6780 + GA5:3:1:161:1744#0/1 +chrM 8749 8825 - GA5:3:1:161:1370#0/1 +chrM 7066 7142 + GA5:3:1:161:786#0/1 +chrM 11180 11256 + GA5:3:1:163:213#0/1 +chrM 8322 8398 + GA5:3:1:163:300#0/1 +chr1 567957 568033 + GA5:3:1:163:493#0/1 +chrM 12819 12895 - GA5:3:1:163:1069#0/1 +chr5 134260214 134260290 + GA5:3:1:165:1929#0/1 +chrM 420 496 + GA5:3:1:164:263#0/1 +chrM 3397 3473 - GA5:3:1:164:1037#0/1 +chrM 9718 9794 - GA5:3:1:166:14#0/1 +chr5 134263411 134263487 - GA5:3:1:167:897#0/1 +chrM 14912 14988 - GA5:3:1:166:1121#0/1 +chr1 568792 568868 - GA5:3:1:168:466#0/1 +chrM 14376 14452 - GA5:3:1:169:469#0/1 +chrM 15473 15549 - GA5:3:1:170:1990#0/1 +chrM 4212 4288 + GA5:3:1:168:531#0/1 +chrM 235 311 + GA5:3:1:169:257#0/1 +chrM 5094 5170 + GA5:3:1:170:206#0/1 +chrM 4701 4777 - GA5:3:1:174:968#0/1 +chr1 567602 567678 - GA5:3:1:174:359#0/1 +chrM 10938 11014 + GA5:3:1:174:1235#0/1 +chrM 420 496 + GA5:3:1:174:1870#0/1 +chrM 5114 5190 + GA5:3:1:175:842#0/1 +chrM 11791 11867 - GA5:3:1:176:1895#0/1 +chrM 11390 11466 + GA5:3:1:179:872#0/1 +chrM 1225 1301 - GA5:3:1:178:724#0/1 +chrM 3047 3123 - GA5:3:1:180:469#0/1 +chrM 4385 4461 - GA5:3:1:179:0#0/1 +chrM 11200 11276 - GA5:3:1:183:1380#0/1 +chrM 3851 3927 - GA5:3:1:181:113#0/1 +chrM 4926 5002 + GA5:3:1:183:1147#0/1 +chrM 2816 2892 + GA5:3:1:178:594#0/1 +chrM 7291 7367 + GA5:3:1:184:1316#0/1 +chrM 11092 11168 - GA5:3:1:184:595#0/1 +chrM 26 102 + GA5:3:1:184:321#0/1 +chrM 10355 10431 + GA5:3:1:185:1665#0/1 +chrM 1568 1644 + GA5:3:1:185:1489#0/1 +chrM 11392 11468 + GA5:3:1:186:48#0/1 +chrM 5798 5874 - GA5:3:1:186:1149#0/1 +chrM 14694 14770 + GA5:3:1:185:695#0/1 +chrM 13875 13951 - GA5:3:1:186:79#0/1 +chr1 567902 567978 - GA5:3:1:188:1579#0/1 +chr1 568804 568880 - GA5:3:1:188:143#0/1 +chrM 4812 4888 - GA5:3:1:189:54#0/1 +chr1 568073 568149 + GA5:3:1:190:47#0/1 +chrM 4558 4634 - GA5:3:1:190:942#0/1 +chrM 6420 6496 + GA5:3:1:190:1501#0/1 +chrM 12281 12357 + GA5:3:1:190:10#0/1 +chr1 567571 567647 - GA5:3:1:190:115#0/1 +chrM 4033 4109 - GA5:3:1:191:1028#0/1 +chrM 15496 15572 + GA5:3:1:191:679#0/1 +chrM 3602 3678 + GA5:3:1:191:1675#0/1 +chrM 9106 9182 - GA5:3:1:191:1941#0/1 +chr5 134263406 134263482 - GA5:3:1:192:946#0/1 +chrM 16051 16127 - GA5:3:1:192:307#0/1 +chrM 10840 10916 + GA5:3:1:192:907#0/1 +chrM 6801 6877 + GA5:3:1:192:632#0/1 +chrM 2799 2875 - GA5:3:1:193:1404#0/1 +chrM 12419 12495 + GA5:3:1:193:1223#0/1 +chrM 1101 1177 + GA5:3:1:194:286#0/1 +chrM 10421 10497 + GA5:3:1:194:290#0/1 +chrM 11275 11351 - GA5:3:1:194:1585#0/1 +chrM 11075 11151 + GA5:3:1:195:193#0/1 +chrM 7886 7962 - GA5:3:1:194:1786#0/1 +chrM 16033 16109 + GA5:3:1:196:162#0/1 +chrM 4255 4331 - GA5:3:1:195:1872#0/1 +chrM 13766 13842 - GA5:3:1:196:137#0/1 +chrM 15943 16019 - GA5:3:1:196:1042#0/1 +chrM 6064 6140 - GA5:3:1:196:1036#0/1 +chr1 567894 567970 + GA5:3:1:196:367#0/1 +chrM 10668 10744 - GA5:3:1:197:1705#0/1 +chrM 8496 8572 + GA5:3:1:198:1613#0/1 +chrM 16271 16347 - GA5:3:1:196:1626#0/1 +chr1 569382 569458 - GA5:3:1:199:1635#0/1 +chrM 7950 8026 - GA5:3:1:200:1321#0/1 +chrM 7717 7793 + GA5:3:1:201:872#0/1 +chrM 9241 9317 - GA5:3:1:202:100#0/1 +chrM 13783 13859 - GA5:3:1:202:706#0/1 +chrM 4885 4961 - GA5:3:1:202:865#0/1 +chrM 3929 4005 - GA5:3:1:203:1231#0/1 +chrM 3741 3817 + GA5:3:1:204:528#0/1 +chr9 33658974 33659050 - GA5:3:1:204:1789#0/1 +chrM 11889 11965 + GA5:3:1:205:1026#0/1 +chrM 13119 13195 - GA5:3:1:204:1298#0/1 +chrM 3874 3950 + GA5:3:1:206:68#0/1 +chrM 3422 3498 + GA5:3:1:201:1544#0/1 +chr5 134259813 134259889 - GA5:3:1:206:918#0/1 +chrM 15043 15119 + GA5:3:1:206:600#0/1 +chrM 6634 6710 - GA5:3:1:206:155#0/1 +chrM 11221 11297 + GA5:3:1:206:1358#0/1 +chrM 13462 13538 + GA5:3:1:206:749#0/1 +chrM 10796 10872 + GA5:3:1:207:1409#0/1 +chrM 5955 6031 + GA5:3:1:208:683#0/1 +chr11 10529688 10529764 - GA5:3:1:207:1021#0/1 +chrM 2862 2938 - GA5:3:1:207:1762#0/1 +chrM 8157 8233 + GA5:3:1:209:281#0/1 +chrM 6781 6857 + GA5:3:1:208:655#0/1 +chr1 567555 567631 + GA5:3:1:210:1081#0/1 +chrM 2089 2165 - GA5:3:1:208:1256#0/1 +chrM 10663 10739 - GA5:3:1:210:680#0/1 +chrM 13240 13316 - GA5:3:1:211:142#0/1 +chrM 15437 15513 + GA5:3:1:212:1819#0/1 +chr1 566620 566696 + GA5:3:1:212:226#0/1 +chrM 5680 5756 - GA5:3:1:212:276#0/1 +chrM 77 153 - GA5:3:1:210:1710#0/1 +chrM 9139 9215 + GA5:3:1:213:1377#0/1 +chr1 564695 564771 + GA5:3:1:214:617#0/1 +chrM 3155 3231 + GA5:3:1:214:175#0/1 +chrM 2816 2892 + GA5:3:1:214:1567#0/1 +chrM 7477 7553 + GA5:3:1:214:262#0/1 +chrM 8879 8955 + GA5:3:1:214:933#0/1 +chrM 8860 8936 + GA5:3:1:214:217#0/1 +chrM 4706 4782 + GA5:3:1:216:1701#0/1 +chrM 6466 6542 - GA5:3:1:217:891#0/1 +chrM 13439 13515 + GA5:3:1:215:1144#0/1 +chrM 4166 4242 + GA5:3:1:217:568#0/1 +chrM 9147 9223 - GA5:3:1:217:1664#0/1 +chr3 96336311 96336387 - GA5:3:1:217:1833#0/1 +chrM 9272 9348 - GA5:3:1:218:216#0/1 +chrM 10928 11004 - GA5:3:1:218:1358#0/1 +chrM 5040 5116 + GA5:3:1:218:1630#0/1 +chrM 10030 10106 + GA5:3:1:219:1693#0/1 +chrM 14452 14528 - GA5:3:1:219:677#0/1 +chrM 13808 13884 - GA5:3:1:219:1089#0/1 +chrM 310 386 - GA5:3:1:220:1479#0/1 +chrM 6445 6521 - GA5:3:1:220:184#0/1 +chrM 9707 9783 - GA5:3:1:221:910#0/1 +chrM 6447 6523 - GA5:3:1:221:216#0/1 +chrM 7578 7654 + GA5:3:1:221:1614#0/1 +chrM 4896 4972 + GA5:3:1:221:147#0/1 +chrM 11515 11591 - GA5:3:1:223:1221#0/1 +chrM 10946 11022 - GA5:3:1:222:1733#0/1 +chrM 6842 6918 + GA5:3:1:225:1169#0/1 +chrM 495 571 + GA5:3:1:220:485#0/1 +chrM 5505 5581 - GA5:3:1:224:1266#0/1 +chrM 11721 11797 + GA5:3:1:219:833#0/1 +chrM 15651 15727 - GA5:3:1:225:1130#0/1 +chrM 2110 2186 + GA5:3:1:226:398#0/1 +chr1 568855 568931 - GA5:3:1:227:1794#0/1 +chrM 8051 8127 - GA5:3:1:227:995#0/1 +chrM 14308 14384 - GA5:3:1:225:1174#0/1 +chr1 567878 567954 + GA5:3:1:227:1815#0/1 +chrM 6304 6380 - GA5:3:1:229:1982#0/1 +chrM 7969 8045 - GA5:3:1:228:1113#0/1 +chrM 6293 6369 - GA5:3:1:230:1016#0/1 +chrM 818 894 + GA5:3:1:231:1353#0/1 +chrM 14261 14337 - GA5:3:1:232:1298#0/1 +chrM 11374 11450 + GA5:3:1:232:514#0/1 +chrM 8045 8121 - GA5:3:1:233:1217#0/1 +chrM 8681 8757 + GA5:3:1:232:1971#0/1 +chrM 3486 3562 - GA5:3:1:233:1277#0/1 +chr1 566494 566570 + GA5:3:1:233:903#0/1 +chrM 9878 9954 - GA5:3:1:233:970#0/1 +chr1 564505 564581 + GA5:3:1:234:1415#0/1 +chrM 11417 11493 + GA5:3:1:234:1143#0/1 +chrM 15652 15728 + GA5:3:1:235:1863#0/1 +chrM 5104 5180 + GA5:3:1:235:1036#0/1 +chrM 3164 3240 + GA5:3:1:235:1129#0/1 +chrM 11719 11795 - GA5:3:1:235:4#0/1 +chrM 395 471 + GA5:3:1:235:1636#0/1 +chrM 3166 3242 + GA5:3:1:236:962#0/1 +chrM 9042 9118 + GA5:3:1:233:1838#0/1 +chrM 10915 10991 + GA5:3:1:235:1166#0/1 +chrM 8037 8113 - GA5:3:1:237:525#0/1 +chrM 10604 10680 - GA5:3:1:237:37#0/1 +chrM 15976 16052 + GA5:3:1:237:967#0/1 +chrM 7775 7851 - GA5:3:1:237:1496#0/1 +chrM 11581 11657 - GA5:3:1:237:1125#0/1 +chrM 773 849 - GA5:3:1:239:1057#0/1 +chrM 16288 16364 - GA5:3:1:238:1759#0/1 +chrM 1281 1357 + GA5:3:1:239:855#0/1 +chrM 1657 1733 + GA5:3:1:240:348#0/1 +chrM 10176 10252 - GA5:3:1:240:94#0/1 +chrM 3185 3261 - GA5:3:1:241:1734#0/1 +chrM 6377 6453 - GA5:3:1:241:968#0/1 +chrM 11399 11475 + GA5:3:1:244:198#0/1 +chrM 10678 10754 - GA5:3:1:244:1599#0/1 +chrM 1452 1528 - GA5:3:1:244:1912#0/1 +chrM 11618 11694 - GA5:3:1:245:362#0/1 +chrM 13579 13655 - GA5:3:1:244:1135#0/1 +chrM 15858 15934 + GA5:3:1:244:1621#0/1 +chrM 9293 9369 - GA5:3:1:245:1065#0/1 +chrM 1083 1159 + GA5:3:1:246:764#0/1 +chrM 2816 2892 + GA5:3:1:246:701#0/1 +chrM 2730 2806 + GA5:3:1:247:437#0/1 +chrM 8902 8978 + GA5:3:1:247:26#0/1 +chrM 4252 4328 + GA5:3:1:247:820#0/1 +chrM 11609 11685 - GA5:3:1:248:1725#0/1 +chrM 10880 10956 + GA5:3:1:247:565#0/1 +chrM 13288 13364 - GA5:3:1:250:163#0/1 +chrM 676 752 + GA5:3:1:250:1216#0/1 +chrM 793 869 - GA5:3:1:250:872#0/1 +chrM 8931 9007 + GA5:3:1:252:1164#0/1 +chrM 3544 3620 + GA5:3:1:251:243#0/1 +chrM 3696 3772 + GA5:3:1:253:1759#0/1 +chrM 9368 9444 - GA5:3:1:253:92#0/1 +chrM 2816 2892 + GA5:3:1:255:789#0/1 +chrM 9102 9178 + GA5:3:1:252:1110#0/1 +chrM 2980 3056 - GA5:3:1:254:530#0/1 +chr1 567271 567347 + GA5:3:1:256:840#0/1 +chrM 9582 9658 - GA5:3:1:255:732#0/1 +chrM 13325 13401 - GA5:3:1:256:794#0/1 +chrM 7896 7972 + GA5:3:1:258:1864#0/1 +chrM 3345 3421 - GA5:3:1:257:1754#0/1 +chrM 16365 16441 + GA5:3:1:258:566#0/1 +chrM 10811 10887 - GA5:3:1:257:1992#0/1 +chr1 569902 569978 - GA5:3:1:259:193#0/1 +chrM 3314 3390 - GA5:3:1:259:466#0/1 +chrM 15883 15959 - GA5:3:1:259:841#0/1 +chr1 564724 564800 - GA5:3:1:259:1579#0/1 +chrM 4714 4790 - GA5:3:1:261:1344#0/1 +chrM 16468 16544 - GA5:3:1:261:260#0/1 +chrM 6558 6634 - GA5:3:1:262:807#0/1 +chrM 8279 8355 + GA5:3:1:262:1989#0/1 +chrM 1881 1957 + GA5:3:1:263:989#0/1 +chrM 10313 10389 - GA5:3:1:263:1859#0/1 +chrM 12145 12221 + GA5:3:1:265:357#0/1 +chrM 12198 12274 + GA5:3:1:265:1168#0/1 +chrM 13527 13603 - GA5:3:1:266:1591#0/1 +chrM 11054 11130 - GA5:3:1:267:532#0/1 +chrM 2819 2895 + GA5:3:1:267:178#0/1 +chrM 15764 15840 + GA5:3:1:268:587#0/1 +chrM 13208 13284 + GA5:3:1:261:133#0/1 +chrM 516 592 + GA5:3:1:268:1979#0/1 +chrM 14986 15062 + GA5:3:1:265:1679#0/1 +chrM 6236 6312 + GA5:3:1:269:0#0/1 +chrM 9719 9795 + GA5:3:1:271:508#0/1 +chrM 10293 10369 - GA5:3:1:273:745#0/1 +chrM 11050 11126 + GA5:3:1:273:1161#0/1 +chrM 1352 1428 - GA5:3:1:273:1629#0/1 +chrM 843 919 + GA5:3:1:273:1611#0/1 +chr5 79947252 79947328 - GA5:3:1:273:1624#0/1 +chrM 4199 4275 - GA5:3:1:273:1799#0/1 +chrM 14674 14750 - GA5:3:1:274:687#0/1 +chrM 15289 15365 - GA5:3:1:275:50#0/1 +chrM 13553 13629 - GA5:3:1:275:1970#0/1 +chrM 2816 2892 + GA5:3:1:277:718#0/1 +chrM 10274 10350 - GA5:3:1:276:84#0/1 +chrM 691 767 - GA5:3:1:276:1892#0/1 +chrM 3523 3599 + GA5:3:1:277:1982#0/1 +chr1 567903 567979 + GA5:3:1:276:1692#0/1 +chrM 11291 11367 + GA5:3:1:277:1664#0/1 +chrM 9494 9570 - GA5:3:1:277:675#0/1 +chrM 9917 9993 - GA5:3:1:279:1440#0/1 +chrM 2184 2260 + GA5:3:1:280:910#0/1 +chrM 2202 2278 - GA5:3:1:281:1665#0/1 +chrM 14827 14903 + GA5:3:1:281:1721#0/1 +chrM 9116 9192 - GA5:3:1:281:1007#0/1 +chrM 12049 12125 - GA5:3:1:281:410#0/1 +chr6 62284081 62284157 + GA5:3:1:281:1663#0/1 +chrM 8153 8229 + GA5:3:1:282:874#0/1 +chrM 6592 6668 - GA5:3:1:281:517#0/1 +chrM 7578 7654 + GA5:3:1:283:920#0/1 +chrM 3314 3390 - GA5:3:1:284:512#0/1 +chrM 12063 12139 - GA5:3:1:285:1895#0/1 +chrM 7082 7158 - GA5:3:1:283:1465#0/1 +chrM 13050 13126 - GA5:3:1:285:854#0/1 +chrM 3747 3823 - GA5:3:1:285:1775#0/1 +chrM 10833 10909 - GA5:3:1:286:905#0/1 +chrM 10742 10818 - GA5:3:1:289:717#0/1 +chrM 11066 11142 - GA5:3:1:290:290#0/1 +chrM 2816 2892 + GA5:3:1:290:211#0/1 +chrM 3553 3629 - GA5:3:1:291:533#0/1 +chr1 569068 569144 - GA5:3:1:291:102#0/1 +chrM 9590 9666 + GA5:3:1:292:1628#0/1 +chrM 2048 2124 - GA5:3:1:291:832#0/1 +chrM 9815 9891 + GA5:3:1:292:992#0/1 +chrM 3314 3390 - GA5:3:1:292:1448#0/1 +chrM 13055 13131 + GA5:3:1:293:912#0/1 +chrM 2760 2836 - GA5:3:1:294:548#0/1 +chrM 3779 3855 - GA5:3:1:294:1438#0/1 +chrM 10951 11027 - GA5:3:1:294:431#0/1 +chrM 1532 1608 - GA5:3:1:295:1615#0/1 +chrM 11772 11848 + GA5:3:1:296:711#0/1 +chrM 1359 1435 + GA5:3:1:295:1527#0/1 +chrM 15988 16064 - GA5:3:1:298:1240#0/1 +chrM 4956 5032 + GA5:3:1:299:1039#0/1 +chrM 2963 3039 - GA5:3:1:297:1448#0/1 +chr1 567336 567412 - GA5:3:1:300:1225#0/1 +chrM 2110 2186 - GA5:3:1:301:1093#0/1 +chrM 3258 3334 + GA5:3:1:301:1802#0/1 +chr5 134263454 134263530 - GA5:3:1:301:1236#0/1 +chrM 8869 8945 + GA5:3:1:301:363#0/1 +chrM 9229 9305 + GA5:3:1:301:751#0/1 +chrM 6579 6655 - GA5:3:1:302:403#0/1 +chrM 5779 5855 - GA5:3:1:302:560#0/1 +chrM 12474 12550 + GA5:3:1:302:1689#0/1 +chrM 2034 2110 - GA5:3:1:302:958#0/1 +chrM 3141 3217 - GA5:3:1:303:1216#0/1 +chrM 12218 12294 - GA5:3:1:304:1597#0/1 +chrM 9137 9213 + GA5:3:1:304:715#0/1 +chrM 942 1018 - GA5:3:1:304:207#0/1 +chrM 2929 3005 + GA5:3:1:306:340#0/1 +chrM 1414 1490 - GA5:3:1:307:1969#0/1 +chrM 5327 5403 - GA5:3:1:307:1941#0/1 +chr17 22023721 22023797 - GA5:3:1:309:428#0/1 +chrM 11067 11143 + GA5:3:1:310:278#0/1 +chrM 12329 12405 + GA5:3:1:312:1973#0/1 +chrM 12612 12688 + GA5:3:1:310:1459#0/1 +chr1 567541 567617 + GA5:3:1:313:706#0/1 +chrM 2818 2894 + GA5:3:1:314:1246#0/1 +chrM 12488 12564 - GA5:3:1:313:1472#0/1 +chrM 5293 5369 + GA5:3:1:315:338#0/1 +chrM 8194 8270 + GA5:3:1:314:132#0/1 +chrM 11313 11389 - GA5:3:1:316:472#0/1 +chrM 15065 15141 - GA5:3:1:316:1193#0/1 +chrM 14965 15041 - GA5:3:1:315:772#0/1 +chrM 10333 10409 - GA5:3:1:314:418#0/1 +chrM 8351 8427 + GA5:3:1:316:938#0/1 +chrM 3535 3611 - GA5:3:1:316:1359#0/1 +chrM 6366 6442 - GA5:3:1:317:1923#0/1 +chrM 2738 2814 - GA5:3:1:317:60#0/1 +chr17 22023745 22023821 + GA5:3:1:316:537#0/1 +chrM 16084 16160 - GA5:3:1:317:897#0/1 +chr1 569903 569979 + GA5:3:1:318:574#0/1 +chrM 832 908 - GA5:3:1:318:1958#0/1 +chrM 5348 5424 - GA5:3:1:318:305#0/1 +chrM 15288 15364 - GA5:3:1:319:671#0/1 +chrM 12508 12584 - GA5:3:1:319:15#0/1 +chrM 5346 5422 + GA5:3:1:320:1170#0/1 +chrM 5850 5926 - GA5:3:1:320:1921#0/1 +chrM 7255 7331 - GA5:3:1:318:1966#0/1 +chrM 13798 13874 + GA5:3:1:320:1346#0/1 +chr1 564464 564540 - GA5:3:1:320:380#0/1 +chrM 8421 8497 + GA5:3:1:322:241#0/1 +chrM 6910 6986 - GA5:3:1:322:946#0/1 +chrM 15124 15200 - GA5:3:1:322:1386#0/1 +chrM 7287 7363 + GA5:3:1:323:711#0/1 +chrM 4946 5022 + GA5:3:1:324:1685#0/1 +chrM 14314 14390 + GA5:3:1:324:375#0/1 +chrM 15363 15439 - GA5:3:1:324:1120#0/1 +chrM 2346 2422 + GA5:3:1:319:1499#0/1 +chrM 11124 11200 + GA5:3:1:324:466#0/1 +chr1 567514 567590 + GA5:3:1:324:1231#0/1 +chrM 4665 4741 - GA5:3:1:325:1750#0/1 +chrM 3366 3442 - GA5:3:1:325:41#0/1 +chr1 569857 569933 - GA5:3:1:325:13#0/1 +chrM 4786 4862 - GA5:3:1:325:1334#0/1 +chrM 3536 3612 - GA5:3:1:326:1009#0/1 +chrM 8273 8349 - GA5:3:1:326:785#0/1 +chrM 10604 10680 + GA5:3:1:326:827#0/1 +chrM 8343 8419 + GA5:3:1:325:1773#0/1 +chrM 7121 7197 - GA5:3:1:326:1761#0/1 +chrM 2816 2892 + GA5:3:1:327:1725#0/1 +chrM 1589 1665 - GA5:3:1:327:1413#0/1 +chrM 5372 5448 - GA5:3:1:327:426#0/1 +chr1 568483 568559 - GA5:3:1:329:486#0/1 +chrM 15853 15929 - GA5:3:1:328:806#0/1 +chrM 2861 2937 + GA5:3:1:329:1087#0/1 +chrM 7209 7285 + GA5:3:1:329:842#0/1 +chrM 9836 9912 - GA5:3:1:329:478#0/1 +chrM 12185 12261 - GA5:3:1:330:1136#0/1 +chrM 13832 13908 - GA5:3:1:330:166#0/1 +chrM 7789 7865 + GA5:3:1:331:1027#0/1 +chrM 4318 4394 - GA5:3:1:331:810#0/1 +chrM 9787 9863 + GA5:3:1:331:278#0/1 +chrM 14017 14093 - GA5:3:1:331:1947#0/1 +chrM 13058 13134 - GA5:3:1:332:325#0/1 +chrM 6046 6122 - GA5:3:1:333:155#0/1 +chrM 2350 2426 + GA5:3:1:327:364#0/1 +chrM 7201 7277 - GA5:3:1:333:1601#0/1 +chrM 11145 11221 + GA5:3:1:334:1026#0/1 +chrM 6757 6833 - GA5:3:1:333:1545#0/1 +chrM 9485 9561 + GA5:3:1:335:1755#0/1 +chrM 12688 12764 - GA5:3:1:335:1597#0/1 +chrM 5083 5159 + GA5:3:1:335:941#0/1 +chrM 11354 11430 - GA5:3:1:336:1945#0/1 +chrM 16485 16561 - GA5:3:1:336:87#0/1 +chrM 12347 12423 + GA5:3:1:336:221#0/1 +chrM 7204 7280 + GA5:3:1:336:1091#0/1 +chrM 8040 8116 - GA5:3:1:336:1916#0/1 +chrM 3701 3777 - GA5:3:1:336:531#0/1 +chrM 400 476 - GA5:3:1:337:420#0/1 +chrM 10483 10559 + GA5:3:1:338:1754#0/1 +chr1 569286 569362 - GA5:3:1:338:1991#0/1 +chrM 7122 7198 - GA5:3:1:339:1836#0/1 +chrM 7081 7157 - GA5:3:1:339:1286#0/1 +chr5 134259841 134259917 - GA5:3:1:340:1081#0/1 +chrM 10965 11041 + GA5:3:1:340:385#0/1 +chrM 708 784 + GA5:3:1:341:78#0/1 +chrM 4655 4731 - GA5:3:1:341:366#0/1 +chrM 1182 1258 - GA5:3:1:342:1207#0/1 +chrM 2748 2824 + GA5:3:1:342:1904#0/1 +chr1 565770 565846 + GA5:3:1:342:1812#0/1 +chrM 5147 5223 + GA5:3:1:344:169#0/1 +chrM 5507 5583 + GA5:3:1:343:17#0/1 +chrM 1750 1826 - GA5:3:1:343:800#0/1 +chrM 11017 11093 - GA5:3:1:344:692#0/1 +chrM 11224 11300 - GA5:3:1:345:1886#0/1 +chrM 3825 3901 - GA5:3:1:346:432#0/1 +chrM 15613 15689 - GA5:3:1:349:1448#0/1 +chrM 7536 7612 - GA5:3:1:347:786#0/1 +chrM 13045 13121 - GA5:3:1:349:804#0/1 +chrM 14403 14479 - GA5:3:1:349:1239#0/1 +chrM 12541 12617 - GA5:3:1:350:754#0/1 +chrM 13561 13637 - GA5:3:1:350:38#0/1 +chrM 110 186 + GA5:3:1:350:918#0/1 +chrM 7145 7221 - GA5:3:1:351:999#0/1 +chr17 22023719 22023795 - GA5:3:1:351:950#0/1 +chrM 3397 3473 - GA5:3:1:352:1006#0/1 +chrM 3390 3466 + GA5:3:1:351:312#0/1 +chrM 2344 2420 - GA5:3:1:352:1832#0/1 +chrM 7891 7967 - GA5:3:1:352:1360#0/1 +chrM 10934 11010 - GA5:3:1:353:352#0/1 +chrM 15433 15509 - GA5:3:1:352:63#0/1 +chrM 3337 3413 + GA5:3:1:353:844#0/1 +chrM 6474 6550 - GA5:3:1:354:1491#0/1 +chrM 11837 11913 + GA5:3:1:353:1239#0/1 +chrM 13862 13938 + GA5:3:1:354:768#0/1 +chrM 5411 5487 - GA5:3:1:354:27#0/1 +chrM 10514 10590 + GA5:3:1:354:1355#0/1 +chrM 8413 8489 + GA5:3:1:356:1541#0/1 +chrM 15375 15451 - GA5:3:1:356:1351#0/1 +chr1 569717 569793 + GA5:3:1:356:611#0/1 +chrM 11380 11456 + GA5:3:1:357:1820#0/1 +chr1 566164 566240 - GA5:3:1:357:1690#0/1 +chr1 566667 566743 + GA5:3:1:357:1552#0/1 +chrM 3173 3249 + GA5:3:1:358:1526#0/1 +chrM 10233 10309 - GA5:3:1:358:1454#0/1 +chrM 3992 4068 - GA5:3:1:358:1695#0/1 +chrM 16338 16414 + GA5:3:1:359:766#0/1 +chrM 9010 9086 - GA5:3:1:358:230#0/1 +chrM 12729 12805 + GA5:3:1:356:1079#0/1 +chrM 6394 6470 - GA5:3:1:359:1358#0/1 +chrM 6142 6218 + GA5:3:1:360:524#0/1 +chrM 4363 4439 - GA5:3:1:361:850#0/1 +chrM 2944 3020 - GA5:3:1:361:1260#0/1 +chr5 134263378 134263454 - GA5:3:1:359:470#0/1 +chrM 13831 13907 - GA5:3:1:362:271#0/1 +chrM 13023 13099 - GA5:3:1:362:103#0/1 +chrM 10640 10716 + GA5:3:1:362:514#0/1 +chrM 2145 2221 - GA5:3:1:362:795#0/1 +chrM 12006 12082 - GA5:3:1:362:1043#0/1 +chrM 5093 5169 - GA5:3:1:363:1544#0/1 +chrM 9773 9849 + GA5:3:1:363:1013#0/1 +chrM 1591 1667 + GA5:3:1:363:1219#0/1 +chrM 443 519 + GA5:3:1:363:1680#0/1 +chrM 10852 10928 - GA5:3:1:362:1409#0/1 +chrM 16255 16331 - GA5:3:1:363:1573#0/1 +chrM 15014 15090 + GA5:3:1:363:392#0/1 +chrM 11515 11591 - GA5:3:1:364:678#0/1 +chrM 2816 2892 + GA5:3:1:364:591#0/1 +chrM 12031 12107 + GA5:3:1:364:940#0/1 +chrM 3700 3776 + GA5:3:1:364:738#0/1 +chrM 7218 7294 - GA5:3:1:364:1037#0/1 +chrM 3314 3390 - GA5:3:1:365:1803#0/1 +chrM 3935 4011 - GA5:3:1:365:1779#0/1 +chrM 9536 9612 - GA5:3:1:365:997#0/1 +chrM 3994 4070 - GA5:3:1:365:284#0/1 +chrM 9513 9589 + GA5:3:1:365:1695#0/1 +chrM 4616 4692 - GA5:3:1:365:754#0/1 +chr11 10530763 10530839 + GA5:3:1:367:1331#0/1 +chrM 13156 13232 + GA5:3:1:367:431#0/1 +chrM 12212 12288 + GA5:3:1:369:624#0/1 +chrM 1964 2040 - GA5:3:1:369:1920#0/1 +chr1 567269 567345 - GA5:3:1:369:424#0/1 +chrM 5448 5524 + GA5:3:1:370:1782#0/1 +chrM 978 1054 - GA5:3:1:370:600#0/1 +chrM 4651 4727 - GA5:3:1:370:288#0/1 +chr3 96336206 96336282 - GA5:3:1:370:1039#0/1 +chrM 10537 10613 + GA5:3:1:370:1508#0/1 +chrM 10640 10716 + GA5:3:1:370:534#0/1 +chrM 12895 12971 - GA5:3:1:370:355#0/1 +chr1 566580 566656 + GA5:3:1:371:462#0/1 +chrM 2816 2892 + GA5:3:1:373:1838#0/1 +chrM 7637 7713 - GA5:3:1:372:98#0/1 +chrM 3874 3950 + GA5:3:1:374:721#0/1 +chr5 134263381 134263457 - GA5:3:1:372:440#0/1 +chr5 79947212 79947288 - GA5:3:1:374:1080#0/1 +chrM 3041 3117 + GA5:3:1:375:1437#0/1 +chr1 564478 564554 - GA5:3:1:375:612#0/1 +chrM 8018 8094 - GA5:3:1:376:1174#0/1 +chrM 11377 11453 + GA5:3:1:376:67#0/1 +chrM 2600 2676 - GA5:3:1:376:558#0/1 +chrM 6442 6518 + GA5:3:1:377:685#0/1 +chrM 465 541 + GA5:3:1:376:1630#0/1 +chrM 10317 10393 - GA5:3:1:377:444#0/1 +chrM 13465 13541 - GA5:3:1:377:1241#0/1 +chrM 2687 2763 - GA5:3:1:378:252#0/1 +chrM 1579 1655 + GA5:3:1:379:967#0/1 +chrM 5460 5536 + GA5:3:1:383:215#0/1 +chrM 54 130 + GA5:3:1:381:1161#0/1 +chrM 8424 8500 - GA5:3:1:383:837#0/1 +chrM 6234 6310 - GA5:3:1:384:782#0/1 +chrM 11515 11591 - GA5:3:1:384:317#0/1 +chrM 3784 3860 - GA5:3:1:385:117#0/1 +chrM 2816 2892 + GA5:3:1:385:153#0/1 +chrM 8859 8935 + GA5:3:1:385:1135#0/1 +chrM 5082 5158 + GA5:3:1:386:1152#0/1 +chrM 6666 6742 + GA5:3:1:387:1466#0/1 +chrM 14287 14363 + GA5:3:1:387:1263#0/1 +chrM 4369 4445 + GA5:3:1:386:884#0/1 +chrM 12361 12437 + GA5:3:1:389:597#0/1 +chrM 3314 3390 - GA5:3:1:389:1104#0/1 +chrM 2148 2224 + GA5:3:1:390:1824#0/1 +chr5 134259835 134259911 + GA5:3:1:390:1946#0/1 +chrM 12519 12595 - GA5:3:1:391:1187#0/1 +chrM 3582 3658 + GA5:3:1:390:1884#0/1 +chrM 11384 11460 + GA5:3:1:391:272#0/1 +chrM 11431 11507 + GA5:3:1:392:1874#0/1 +chrM 11288 11364 - GA5:3:1:393:162#0/1 +chrM 1805 1881 - GA5:3:1:392:1394#0/1 +chrM 10179 10255 + GA5:3:1:393:1056#0/1 +chrM 3314 3390 - GA5:3:1:393:860#0/1 +chrM 8780 8856 - GA5:3:1:394:1561#0/1 +chrM 3734 3810 + GA5:3:1:395:207#0/1 +chr11 10530095 10530171 + GA5:3:1:390:112#0/1 +chrM 1385 1461 + GA5:3:1:397:1357#0/1 +chrM 9675 9751 + GA5:3:1:398:1207#0/1 +chrM 11084 11160 + GA5:3:1:398:12#0/1 +chrM 8583 8659 + GA5:3:1:399:941#0/1 +chrM 3305 3381 + GA5:3:1:399:1072#0/1 +chrM 8512 8588 - GA5:3:1:399:1299#0/1 +chrM 11287 11363 - GA5:3:1:400:488#0/1 +chrM 4790 4866 + GA5:3:1:399:542#0/1 +chrM 1435 1511 - GA5:3:1:400:748#0/1 +chr1 567255 567331 - GA5:3:1:401:673#0/1 +chrM 566 642 - GA5:3:1:402:1934#0/1 +chrM 13143 13219 - GA5:3:1:402:1807#0/1 +chrM 12171 12247 - GA5:3:1:402:283#0/1 +chrM 11264 11340 + GA5:3:1:399:1484#0/1 +chrM 9209 9285 - GA5:3:1:402:1896#0/1 +chrM 10940 11016 - GA5:3:1:403:1595#0/1 +chrM 11515 11591 - GA5:3:1:404:1551#0/1 +chrM 6685 6761 - GA5:3:1:405:1600#0/1 +chrM 184 260 - GA5:3:1:403:1870#0/1 +chrM 31 107 + GA5:3:1:404:716#0/1 +chrM 11170 11246 + GA5:3:1:405:1184#0/1 +chrM 15089 15165 - GA5:3:1:406:336#0/1 +chrM 8123 8199 - GA5:3:1:405:1223#0/1 +chrM 12144 12220 - GA5:3:1:406:283#0/1 +chrM 5813 5889 - GA5:3:1:406:97#0/1 +chrM 15487 15563 + GA5:3:1:407:686#0/1 +chrM 7975 8051 - GA5:3:1:406:381#0/1 +chrM 14369 14445 + GA5:3:1:407:315#0/1 +chrM 4772 4848 + GA5:3:1:407:846#0/1 +chrM 16483 16559 - GA5:3:1:407:692#0/1 +chrM 8096 8172 - GA5:3:1:408:761#0/1 +chrM 34 110 - GA5:3:1:408:87#0/1 +chrM 10347 10423 + GA5:3:1:408:1553#0/1 +chrM 14112 14188 + GA5:3:1:409:1433#0/1 +chrM 6575 6651 + GA5:3:1:409:571#0/1 +chrM 696 772 + GA5:3:1:412:395#0/1 +chrM 11790 11866 - GA5:3:1:410:1990#0/1 +chrM 16268 16344 - GA5:3:1:411:1317#0/1 +chr13 110076567 110076643 + GA5:3:1:412:346#0/1 +chrM 1687 1763 + GA5:3:1:412:1157#0/1 +chrM 10936 11012 - GA5:3:1:414:1810#0/1 +chrM 3994 4070 + GA5:3:1:414:1062#0/1 +chr1 566609 566685 + GA5:3:1:414:1864#0/1 +chrM 3842 3918 + GA5:3:1:414:976#0/1 +chrM 9306 9382 - GA5:3:1:413:1773#0/1 +chrM 16224 16300 - GA5:3:1:415:897#0/1 +chrM 3903 3979 - GA5:3:1:416:214#0/1 +chrM 2943 3019 - GA5:3:1:415:549#0/1 +chrM 14533 14609 - GA5:3:1:417:1892#0/1 +chrM 11515 11591 - GA5:3:1:417:1023#0/1 +chrM 8482 8558 - GA5:3:1:418:1783#0/1 +chrM 11515 11591 - GA5:3:1:419:1023#0/1 +chr1 565758 565834 + GA5:3:1:419:1785#0/1 +chrM 8485 8561 - GA5:3:1:419:892#0/1 +chrM 3314 3390 - GA5:3:1:420:168#0/1 +chrM 11316 11392 - GA5:3:1:420:617#0/1 +chrM 2370 2446 - GA5:3:1:421:271#0/1 +chrM 14762 14838 + GA5:3:1:417:1426#0/1 +chr1 568483 568559 - GA5:3:1:423:731#0/1 +chrM 3019 3095 + GA5:3:1:424:54#0/1 +chr1 564926 565002 - GA5:3:1:424:1669#0/1 +chrM 12573 12649 - GA5:3:1:424:594#0/1 +chrM 2816 2892 + GA5:3:1:425:382#0/1 +chrM 14111 14187 - GA5:3:1:425:932#0/1 +chrM 2462 2538 - GA5:3:1:425:1589#0/1 +chrM 8469 8545 + GA5:3:1:421:1967#0/1 +chrM 11092 11168 - GA5:3:1:425:162#0/1 +chrM 6473 6549 + GA5:3:1:426:1489#0/1 +chrM 16220 16296 - GA5:3:1:427:1426#0/1 +chrM 4832 4908 + GA5:3:1:427:1780#0/1 +chr17 22023725 22023801 - GA5:3:1:427:1140#0/1 +chr1 567374 567450 - GA5:3:1:427:420#0/1 +chrM 11821 11897 + GA5:3:1:429:1694#0/1 +chrM 8061 8137 - GA5:3:1:430:378#0/1 +chr5 134260199 134260275 - GA5:3:1:429:1507#0/1 +chrM 9877 9953 - GA5:3:1:431:248#0/1 +chrM 11833 11909 + GA5:3:1:428:1466#0/1 +chrM 3658 3734 - GA5:3:1:432:1011#0/1 +chrM 861 937 - GA5:3:1:432:381#0/1 +chrM 5607 5683 + GA5:3:1:432:886#0/1 +chrM 8622 8698 - GA5:3:1:433:1453#0/1 +chrM 9468 9544 + GA5:3:1:433:1188#0/1 +chrM 10362 10438 - GA5:3:1:434:1170#0/1 +chrM 3138 3214 + GA5:3:1:436:428#0/1 +chrM 4320 4396 - GA5:3:1:435:1711#0/1 +chr1 567521 567597 - GA5:3:1:436:1244#0/1 +chrM 8468 8544 + GA5:3:1:437:1704#0/1 +chrM 3891 3967 - GA5:3:1:437:1581#0/1 +chrM 13657 13733 - GA5:3:1:438:1005#0/1 +chrM 9922 9998 - GA5:3:1:439:1607#0/1 +chrM 15865 15941 + GA5:3:1:438:1116#0/1 +chrM 5353 5429 - GA5:3:1:437:120#0/1 +chrM 8744 8820 + GA5:3:1:440:1464#0/1 +chrM 5339 5415 + GA5:3:1:440:140#0/1 +chrM 3734 3810 + GA5:3:1:440:823#0/1 +chrM 4252 4328 + GA5:3:1:441:633#0/1 +chrM 13502 13578 + GA5:3:1:442:1663#0/1 +chrM 16346 16422 + GA5:3:1:443:1999#0/1 --- a/tools/samtools/sam2interval.py Wed Aug 24 15:33:07 2011 -0400 +++ b/tools/samtools/sam2interval.py Wed Aug 24 16:43:02 2011 -0400 @@ -68,7 +68,7 @@ cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' ) - print '#chrom\tstart\tend\tstrand' # provide a (partial) header so that strand is automatically set in metadata + print '#chrom\tstart\tend\tstrand\tread_name' # provide a (partial) header so that strand is automatically set in metadata for line in infile: line = line.rstrip( '\r\n' ) @@ -90,7 +90,7 @@ if options.prt_all: print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line) else: - print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand) + print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, read_name) if __name__ == "__main__": main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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