# HG changeset patch # User devteam # Date 1396357967 14400 # Node ID 56dab41a4c5fe6faf52d59fd5c0726f955791142 Imported from capsule None diff -r 000000000000 -r 56dab41a4c5f featureCounter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featureCounter.py Tue Apr 01 09:12:47 2014 -0400 @@ -0,0 +1,146 @@ +#!/usr/bin/env python +#Guruprasad Ananda +""" +Calculate count and coverage of one query on another, and append the Coverage and counts to +the last four columns as bases covered, percent coverage, number of completely present features, number of partially present/overlapping features. + +usage: %prog bed_file_1 bed_file_2 out_file + -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file + -2, --cols2=N,N,N,N: Columns for chr, start, end, strand in second file +""" +import sys, fileinput +from bx.intervals.io import * +from bx.cookbook import doc_optparse +from bx.intervals.operations import quicksect +from galaxy.tools.util.galaxyops import * + +assert sys.version_info[:2] >= ( 2, 4 ) + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def counter(node, start, end): + global full, partial + if node.start <= start and node.maxend > start: + if node.end >= end or (node.start == start and end > node.end > start): + full += 1 + elif end > node.end > start: + partial += 1 + if node.left and node.left.maxend > start: + counter(node.left, start, end) + if node.right: + counter(node.right, start, end) + elif start < node.start < end: + if node.end <= end: + full += 1 + else: + partial += 1 + if node.left and node.left.maxend > start: + counter(node.left, start, end) + if node.right: + counter(node.right, start, end) + else: + if node.left: + counter(node.left, start, end) + +def count_coverage( readers, comments=True ): + primary = readers[0] + secondary = readers[1] + secondary_copy = readers[2] + + rightTree = quicksect.IntervalTree() + for item in secondary: + if type( item ) is GenomicInterval: + rightTree.insert( item, secondary.linenum, item.fields ) + + bitsets = secondary_copy.binned_bitsets() + + global full, partial + + for interval in primary: + if type( interval ) is Header: + yield interval + if type( interval ) is Comment and comments: + yield interval + elif type( interval ) == GenomicInterval: + chrom = interval.chrom + start = int(interval.start) + end = int(interval.end) + full = 0 + partial = 0 + if chrom not in bitsets: + bases_covered = 0 + percent = 0.0 + full = 0 + partial = 0 + else: + bases_covered = bitsets[ chrom ].count_range( start, end-start ) + if (end - start) == 0: + percent = 0 + else: + percent = float(bases_covered) / float(end - start) + if bases_covered: + root = rightTree.chroms[chrom] #root node for the chrom tree + counter(root, start, end) + interval.fields.append(str(bases_covered)) + interval.fields.append(str(percent)) + interval.fields.append(str(full)) + interval.fields.append(str(partial)) + yield interval + + +def main(): + options, args = doc_optparse.parse( __doc__ ) + + try: + chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) + chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) + in1_fname, in2_fname, out_fname = args + except: + stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." ) + + g1 = NiceReaderWrapper( fileinput.FileInput( in1_fname ), + chrom_col=chr_col_1, + start_col=start_col_1, + end_col=end_col_1, + strand_col=strand_col_1, + fix_strand=True ) + g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ), + chrom_col=chr_col_2, + start_col=start_col_2, + end_col=end_col_2, + strand_col=strand_col_2, + fix_strand=True ) + g2_copy = NiceReaderWrapper( fileinput.FileInput( in2_fname ), + chrom_col=chr_col_2, + start_col=start_col_2, + end_col=end_col_2, + strand_col=strand_col_2, + fix_strand=True ) + + + out_file = open( out_fname, "w" ) + + try: + for line in count_coverage([g1, g2, g2_copy]): + if type( line ) is GenomicInterval: + out_file.write( "%s\n" % "\t".join( line.fields ) ) + else: + out_file.write( "%s\n" % line ) + except ParseError, exc: + out_file.close() + fail( str( exc ) ) + + out_file.close() + + if g1.skipped > 0: + print skipped( g1, filedesc=" of 1st dataset" ) + if g2.skipped > 0: + print skipped( g2, filedesc=" of 2nd dataset" ) + elif g2_copy.skipped > 0: + print skipped( g2_copy, filedesc=" of 2nd dataset" ) + + +if __name__ == "__main__": + main() diff -r 000000000000 -r 56dab41a4c5f featureCounter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featureCounter.xml Tue Apr 01 09:12:47 2014 -0400 @@ -0,0 +1,79 @@ + + + + bx-python + galaxy-ops + + featureCounter.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +This tool finds the coverage of intervals in the first dataset on intervals in the second dataset. The coverage and count are appended as 4 new columns in the resulting dataset. + +----- + +**Example** + +- If **First dataset** consists of the following windows:: + + chrX 1 10001 seg 0 - + chrX 10001 20001 seg 0 - + chrX 20001 30001 seg 0 - + chrX 30001 40001 seg 0 - + +- and **Second dataset** consists of the following exons:: + + chrX 5000 6000 seg2 0 - + chrX 5500 7000 seg2 0 - + chrX 9000 22000 seg2 0 - + chrX 24000 34000 seg2 0 - + chrX 36000 38000 seg2 0 - + +- the **Result** is the coverage of exons of the second dataset in each of the windows contained in first dataset:: + + chrX 1 10001 seg 0 - 3001 0.3001 2 1 + chrX 10001 20001 seg 0 - 10000 1.0 1 0 + chrX 20001 30001 seg 0 - 8000 0.8 0 2 + chrX 30001 40001 seg 0 - 5999 0.5999 1 1 + +- To clarify, the following line of output ( added columns are indexed by a, b and c ):: + + a b c d + chrX 1 10001 seg 0 - 3001 0.3001 2 1 + + implies that 2 exons (c) fall fully in this window (chrX:1-10001), 1 exon (d) partially overlaps this window, and these 3 exons cover 30.01% (c) of the window size, spanning 3001 nucleotides (a). + + * a: number of nucleotides in this window covered by the features in (c) and (d) - features overlapping with each other will be merged to calculate (a) + * b: fraction of window size covered by features in (c) and (d) - features overlapping with each other will be merged to calculate (b) + * c: number of features in the 2nd dataset that fall **completely** within this window + * d: number of features in the 2nd dataset that **partially** overlap this window + + + diff -r 000000000000 -r 56dab41a4c5f test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Apr 01 09:12:47 2014 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 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71 1.0 1 0 +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + 93 1.0 1 0 +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - 0 0.0 0 0 +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - 144 1.0 1 0 +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + 25 1.0 1 0 +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - 106 1.0 1 0 +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + 139 1.0 1 0 +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + 168 1.0 1 0 +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - 230 1.0 1 0 +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + 53 1.0 1 0 +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - 246 1.0 1 0 +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - 186 1.0 1 0 +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + 33 1.0 1 0 +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - 1617 1.0 1 0 +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + 0 0.0 0 0 +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - 0 0.0 0 0 +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + 877 1.0 1 0 +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - 232 1.0 1 0 +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + 25 1.0 1 0 +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - 234 1.0 1 0 diff -r 000000000000 -r 56dab41a4c5f test-data/chrY1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chrY1.bed Tue Apr 01 09:12:47 2014 -0400 @@ -0,0 +1,237 @@ +chrY 132990 160020 uc004fon.1 0 + 140854 156002 0 9 71,203,148,137,129,156,184,296,761, 0,5158,7843,12409,14324,15175,16711,22773,26269, +chrY 138078 156125 uc004foo.1 0 + 140854 156002 0 7 273,148,137,129,156,184,362, 0,2755,7321,9236,10087,11623,17685, +chrY 157538 160020 uc004fop.1 0 + 157538 157538 0 1 2482, 0, +chrY 161425 168795 uc004foq.1 0 - 161740 168184 0 4 439,153,149,710, 0,2601,2973,6660, +chrY 161425 170887 uc004for.1 0 - 161740 170886 0 6 439,153,149,209,159,71, 0,2601,2973,6660,8007,9391, +chrY 214969 222590 uc004fos.1 0 - 215101 221653 0 5 283,107,119,176,549, 0,4369,4543,6530,7072, +chrY 214969 267627 uc004fot.1 0 - 215101 267426 0 13 283,107,119,176,90,49,157,87,75,103,104,186,525, 0,4369,4543,6530,7072,7648,11281,11939,12466,12999,13355,27170,52133, +chrY 505078 527558 uc004fou.1 0 + 511632 525371 0 6 259,709,209,58,89,2433, 0,6122,10274,16477,16655,20047, +chrY 505078 540146 uc004fov.1 0 + 511632 539564 0 6 259,709,209,58,89,627, 0,6122,10274,16477,16655,34441, +chrY 720013 720042 uc004fow.1 0 + 720013 720013 0 1 29, 0, +chrY 1274886 1291530 uc004fox.1 0 - 1274889 1291527 0 6 128,163,134,167,103,82, 0,2532,6385,10439,12812,16562, +chrY 1274886 1291530 uc004foy.1 0 - 1274889 1285338 0 5 128,163,134,167,82, 0,2532,6385,10439,16562, +chrY 1274886 1291530 uc004foz.1 0 - 1274886 1274886 0 6 128,345,134,167,100,82, 0,2777,6385,10439,12812,16562, +chrY 1347700 1388827 uc004fpa.1 0 + 1361596 1388372 0 13 72,88,102,143,124,130,173,134,30,136,97,82,533, 0,5947,13870,16970,19711,19951,21529,25520,26619,31683,35115,36638,40594, +chrY 1347700 1388827 uc004fpb.1 0 + 1361596 1388372 0 13 72,64,102,143,124,130,173,134,30,136,97,82,533, 0,5947,13870,16970,19711,19951,21529,25520,26619,31683,35115,36638,40594, +chrY 1347700 1388827 uc004fpc.1 0 + 1361596 1388482 0 11 72,88,102,143,124,130,173,134,30,136,533, 0,5947,13870,16970,19711,19951,21529,25520,26619,31683,40594, +chrY 1347700 1388827 uc004fpd.1 0 + 1361596 1384394 0 9 72,88,102,143,124,130,173,82,533, 0,5947,13870,16970,19711,19951,21529,36638,40594, +chrY 1361570 1388827 uc004fpe.1 0 + 1361596 1384394 0 10 102,143,124,130,173,134,30,136,82,533, 0,3100,5841,6081,7659,11650,12749,17813,22768,26724, +chrY 1415508 1461582 uc004fpf.1 0 + 1420658 1461358 0 12 311,102,119,115,133,185,116,27,115,106,82,299, 0,5112,8700,11815,15484,15706,19605,22245,28522,42043,44407,45775, +chrY 1465044 1470994 uc004fpg.1 0 - 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7627397 7627397 0 2 131,61, 0,1830, +chrY 7670635 7737302 uc004frg.1 0 - 7670635 7670635 0 5 433,187,195,110,108, 0,33926,34239,62900,66559, +chrY 7732964 7738723 uc004frh.1 0 + 7732964 7732964 0 2 156,822, 0,4937, +chrY 8611410 8611919 uc004fri.1 0 - 8611410 8611410 0 2 63,158, 0,351, +chrY 8632512 8633324 uc004frj.1 0 + 8632512 8632512 0 2 88,181, 0,631, +chrY 8711360 8745423 uc004frk.1 0 - 8711360 8711360 0 5 87,316,303,84,37, 0,568,5680,11541,34026, +chrY 9214669 9220483 uc004frl.1 0 - 9214669 9214669 0 4 31,178,104,114, 0,1931,5124,5700, +chrY 9227488 9232441 uc004frm.1 0 - 9227488 9227488 0 2 177,82, 0,4871, +chrY 9235072 9237886 uc004frn.1 0 + 9235118 9236952 0 7 265,267,78,112,146,93,210, 0,283,1157,1363,1576,1817,2604, +chrY 9235072 9237886 uc004fro.1 0 + 9235118 9237699 0 7 265,267,78,112,146,82,210, 0,283,1157,1363,1576,1828,2604, +chrY 9247188 9273071 uc004frp.1 0 - 9247188 9247188 0 8 60,159,146,102,60,159,146,102, 0,3610,5269,5501,20277,23886,25549,25781, +chrY 9255405 9258201 uc004frq.1 0 + 9255451 9257267 0 6 532,78,112,146,93,210, 0,1139,1345,1558,1799,2586, +chrY 9255405 9258201 uc004frr.1 0 + 9255451 9258014 0 6 532,78,112,146,82,210, 0,1139,1345,1558,1810,2586, +chrY 9275684 9278479 uc004frs.1 0 + 9275684 9275684 0 6 531,78,112,146,93,210, 0,1138,1344,1557,1798,2585, +chrY 9275684 9298825 uc004frt.1 0 + 9296075 9298638 0 12 531,78,112,146,82,210,532,78,112,146,82,210, 0,1138,1344,1557,1809,2585,20345,21484,21690,21903,22155,22931, +chrY 9296029 9298825 uc004fru.1 0 + 9296075 9297891 0 6 532,78,112,146,93,210, 0,1139,1345,1558,1799,2586, +chrY 9906351 9911962 uc004frv.1 0 - 9906351 9906351 0 4 60,159,146,110, 0,3615,5269,5501, +chrY 9914563 9917357 uc004frw.1 0 + 9914609 9917170 0 6 532,78,112,146,82,210, 0,1139,1345,1558,1810,2584, +chrY 9914563 9917357 uc004frx.1 0 + 9914609 9916425 0 6 532,78,112,146,93,210, 0,1139,1345,1558,1799,2584, +chrY 9926661 9932263 uc004fry.1 0 - 9926661 9926661 0 4 60,159,146,102, 0,3611,5268,5500, +chrY 9934894 9937527 uc004frz.1 0 + 9934921 9937502 0 7 246,267,78,112,146,82,48, 0,264,1138,1344,1557,1809,2585, +chrY 9934894 9937527 uc004fsa.1 0 + 9934921 9936755 0 7 246,267,78,112,146,93,48, 0,264,1138,1344,1557,1798,2585, +chrY 9955177 9957971 uc004fsb.1 0 + 9955527 9957037 0 7 246,266,78,112,146,93,210, 0,264,1137,1343,1556,1797,2584, +chrY 9955177 9957971 uc004fsc.1 0 + 9955527 9957784 0 7 246,266,78,112,146,82,210, 0,264,1137,1343,1556,1808,2584, +chrY 9967274 9972885 uc004fsd.1 0 - 9967274 9967274 0 4 60,159,146,110, 0,3610,5269,5501, +chrY 9975488 9978284 uc004fse.1 0 + 9975534 9978097 0 6 532,78,112,146,82,210, 0,1139,1345,1558,1810,2586, +chrY 9975488 9978284 uc004fsf.1 0 + 9975534 9977350 0 6 532,78,112,146,93,210, 0,1139,1345,1558,1799,2586, +chrY 10058329 10062762 uc004fsg.1 0 - 10058329 10058329 0 3 151,102,64, 0,4061,4369, +chrY 10138708 10141308 uc004fsh.1 0 + 10138708 10138708 0 3 136,205,190, 0,613,2410, +chrY 10154432 10162871 uc004fsi.1 0 - 10154432 10154432 0 7 246,256,114,477,75,162,37, 0,492,1721,3752,4917,7299,8402, +chrY 10154432 10162871 uc004fsj.1 0 - 10154432 10154432 0 6 246,114,477,75,162,37, 0,1721,3752,4917,7299,8402, +chrY 10165261 10168905 uc004fsk.1 0 - 10165261 10165261 0 2 105,202, 0,3442, +chrY 10188192 10206085 uc004fsl.1 0 + 10188192 10188192 0 7 1818,87,149,157,79,198,680, 0,4294,11765,12606,15593,15792,17213, +chrY 10200764 10221898 uc004fsm.1 0 - 10200764 10200764 0 5 258,138,109,160,245, 0,7839,10333,17305,20889, +chrY 10248761 10260854 uc004fsn.1 0 + 10248761 10248761 0 5 155,112,75,39,46, 0,3621,8158,8918,12047, +chrY 10358406 10359571 uc004fso.1 0 + 10358406 10358406 0 3 57,146,309, 0,170,856, +chrY 10540971 10542306 uc004fsp.1 0 + 10540971 10540971 0 2 285,158, 0,1177, +chrY 11792095 11792124 uc004fsq.1 0 + 11792095 11792095 0 1 29, 0, +chrY 11794588 11794618 uc004fsr.1 0 - 11794588 11794588 0 1 30, 0, +chrY 13283691 13313547 uc004fss.1 0 + 13283691 13283691 0 4 340,47,94,4761, 0,2273,24144,25095, +chrY 13322553 13482162 uc004fst.1 0 + 13330774 13480735 0 46 825,60,156,149,80,113,219,116,252,139,153,105,207,137,134,88,343,96,212,241,150,121,131,279,126,126,170,109,147,147,223,221,191,174,142,751,124,226,130,186,221,89,157,213,96,1565, 0,7407,8161,19362,20881,23886,25348,34386,34772,35185,36931,38299,55962,57276,59254,69842,72357,74245,75423,76793,77380,78300,84977,85295,89180,90272,91805,108954,109447,110410,111605,114899,117195,132454,136677,138630,139776,141006,141829,145098,145698,146004,155105,155398,156331,158044, +chrY 13525412 13541784 uc004fsu.1 0 + 13526241 13539428 0 18 307,47,58,48,130,156,100,136,86,99,161,145,145,182,118,154,140,2436, 0,827,3429,5252,7732,8620,8856,9611,10457,10777,10960,11523,11776,12154,12410,12800,13296,13936, +chrY 13526170 13541784 uc004fsv.1 0 + 13526241 13539428 0 17 116,58,48,130,156,100,136,86,99,161,145,145,182,118,154,140,2436, 0,2671,4494,6974,7862,8098,8853,9699,10019,10202,10765,11018,11396,11652,12042,12538,13178, +chrY 13855854 13980437 uc004fsw.1 0 - 13855855 13980379 0 18 247,171,127,142,188,115,149,75,65,206,106,130,773,396,96,93,156,76, 0,16436,25697,63126,64376,68296,70818,71457,71605,88974,90020,91640,100982,120422,121342,123296,123883,124507, +chrY 13869656 14101944 uc004fsx.1 0 - 13871129 14100939 0 28 1500,171,127,142,188,115,149,75,65,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157, 0,2634,11895,49324,50574,54494,57016,57655,57803,75172,76218,77838,87180,106620,107540,109494,111384,112047,117884,120873,145476,148535,162610,166352,200634,221738,230871,231131, +chrY 13918782 14101944 uc004fsy.1 0 - 13918976 14100939 0 25 340,188,115,149,75,65,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157, 0,1448,5368,7890,8529,8677,26046,27092,28712,38054,57494,58414,60368,62258,62921,68758,71747,96350,99409,113484,117226,151508,172612,181745,182005, +chrY 13944307 14101944 uc004fsz.1 0 - 13944387 14100939 0 20 335,206,106,130,773,396,96,93,220,99,127,94,35,55,121,59,50,109,64,1157, 0,521,1567,3187,12529,31969,32889,34843,36733,37396,43233,46222,70825,73884,87959,91701,125983,147087,156220,156480, +chrY 14017575 14101944 uc004fta.1 0 - 14018177 14100939 0 7 671,121,59,50,109,64,1157, 0,14691,18433,52715,73819,82952,83212, +chrY 14324840 14327296 uc004ftb.1 0 + 14325609 14326533 0 2 869,798, 0,1658, +chrY 14607045 14607786 uc004ftc.1 0 - 14607144 14607714 0 2 375,174, 0,567, +chrY 14677491 14678232 uc004ftd.1 0 + 14677563 14678133 0 2 174,375, 0,366, +chrY 15144025 15464921 uc004fte.1 0 + 15344422 15462536 0 6 190,60,153,186,790,3235, 0,196707,200365,301436,306978,317661, +chrY 15145019 15464921 uc004ftf.1 0 + 15451113 15462536 0 9 153,571,60,153,111,122,186,790,3235, 0,98275,195713,199371,224873,227935,300442,305984,316667, +chrY 15145019 15464921 uc004ftg.1 0 + 15243393 15462536 0 6 153,571,153,186,790,3235, 0,98275,199371,300442,305984,316667, +chrY 15145847 15464921 uc004fth.1 0 + 15243393 15462536 0 6 363,583,153,186,790,3235, 0,97435,198543,299614,305156,315839, +chrY 15243294 15354818 uc004fti.1 0 + 15243393 15354811 0 4 571,60,153,93, 0,97438,101096,111431, +chrY 18196434 18200747 uc004ftj.1 0 - 18196434 18196434 0 3 207,118,158, 0,1542,4155, +chrY 18390253 18391834 uc004ftk.1 0 - 18390817 18391171 0 1 1581, 0, +chrY 18499533 18501494 uc004ftl.1 0 - 18499540 18501166 0 1 1961, 0, +chrY 18647060 18649021 uc004ftm.1 0 + 18647388 18649014 0 1 1961, 0, +chrY 18756722 18758303 uc004ftn.1 0 + 18757385 18757739 0 1 1581, 0, +chrY 18947806 18952124 uc004fto.1 0 + 18947806 18947806 0 3 158,118,207, 0,2658,4111, +chrY 19167944 19169866 uc004ftp.1 0 + 19168061 19169745 0 2 630,814, 0,1108, +chrY 19167944 19210237 uc004ftq.1 0 + 19168061 19172078 0 6 630,110,87,155,86,428, 0,3443,4112,5246,36002,41865, +chrY 19167944 19210237 uc004ftr.1 0 + 19168061 19209908 0 2 630,428, 0,41865, +chrY 19202479 19211795 uc004fts.1 0 - 19202479 19202479 0 5 1143,137,114,101,142, 0,6206,6925,7400,9174, +chrY 19351155 19360471 uc004ftt.1 0 + 19351155 19351155 0 5 142,101,114,137,1143, 0,1815,2277,2973,8173, +chrY 19352713 19395009 uc004ftu.1 0 - 19390871 19394892 0 6 428,86,155,87,110,630, 0,6205,36891,38093,38743,41666, +chrY 19352713 19395009 uc004ftv.1 0 - 19353042 19394892 0 2 428,630, 0,41666, +chrY 19393087 19395009 uc004ftw.1 0 - 19393208 19394892 0 2 814,630, 0,1292, +chrY 19493774 19499502 uc004ftx.1 0 - 19493774 19493774 0 2 334,1161, 0,4567, +chrY 19553972 19698690 uc004fty.1 0 - 19553972 19553972 0 2 143,372, 0,144346, +chrY 19611913 19614093 uc004ftz.1 0 - 19613740 19613983 0 1 2180, 0, +chrY 20076704 20124427 uc004fua.1 0 - 20076704 20076704 0 9 1434,156,78,122,919,240,264,126,122, 0,3493,3858,9675,11025,18474,19209,24738,47601, +chrY 20076704 20124427 uc004fub.1 0 - 20076704 20076704 0 11 1434,61,156,78,146,122,919,240,264,126,122, 0,1626,3493,3858,4528,9675,11025,18474,19209,24738,47601, +chrY 20188623 20211564 uc004fuc.1 0 + 20208498 20209756 0 4 221,298,1243,208, 0,19860,21020,22733, +chrY 20188655 20211564 uc004fud.1 0 + 20208498 20211377 0 4 101,298,92,208, 0,19828,22139,22701, +chrY 20213723 20225769 uc004fue.1 0 + 20218906 20225394 0 5 365,4267,93,96,699, 0,949,7289,9766,11347, +chrY 20326688 20337013 uc004fuf.1 0 - 20327268 20336982 0 11 931,200,70,600,138,180,139,128,97,148,125, 0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200, +chrY 20326688 20366212 uc004fug.1 0 - 20327268 20365808 0 27 931,200,70,600,138,180,139,359,97,148,125,182,195,120,163,182,159,120,159,146,130,135,171,123,78,169,268, 0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200,10408,10864,11181,15457,15715,26357,26631,27169,29937,30206,34113,35903,36320,37747,38970,39256, +chrY 20342403 20366212 uc004fuh.1 0 - 20342405 20365808 0 11 182,159,120,159,146,130,171,123,78,169,268, 0,10642,10916,11454,14222,14491,20188,20605,22032,23255,23541, +chrY 21021299 21023423 uc004fui.1 0 - 21021299 21021299 0 1 2124, 0, +chrY 21036941 21090502 uc004fuj.1 0 - 21036941 21036941 0 6 155,240,60,110,105,958, 0,760,2521,4204,41684,52603, +chrY 21146998 21164428 uc004fuk.1 0 + 21147145 21163620 0 7 163,84,104,51,82,92,814, 0,3883,6865,8749,12299,13759,16616, +chrY 21146998 21164428 uc004ful.1 0 + 21147145 21163620 0 6 163,84,104,82,92,814, 0,3883,6865,12299,13759,16616, +chrY 21327341 21352306 uc004fum.1 0 + 21327437 21352306 0 7 99,78,181,98,172,158,102, 0,710,3800,5216,12737,23441,24863, +chrY 21966421 21972836 uc004fun.1 0 - 21966473 21972204 0 5 144,89,111,104,86, 0,552,723,5775,6329, +chrY 22082636 22097060 uc004fuo.1 0 + 22084624 22096782 0 12 123,113,104,178,153,115,111,111,111,111,89,577, 0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13347,13847, +chrY 22082636 22097060 uc004fup.1 0 + 22090452 22096782 0 11 123,113,104,153,115,111,111,111,111,89,577, 0,1984,2571,7787,9950,11020,11572,12117,13149,13347,13847, +chrY 22106177 22120600 uc004fuq.1 0 + 22108165 22120322 0 12 123,113,104,178,153,115,111,111,111,111,89,577, 0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13346,13846, +chrY 22106177 22120600 uc004fur.1 0 + 22113993 22120322 0 11 123,113,104,153,115,111,111,111,111,89,577, 0,1984,2571,7787,9950,11020,11572,12117,13149,13346,13846, +chrY 22154873 22165940 uc004fus.1 0 - 22154873 22154873 0 6 63,92,162,99,162,81, 0,1183,3901,5672,6366,10986, +chrY 22381088 22702366 uc004fut.1 0 + 22381088 22381088 0 4 25,114,138,239, 0,319412,319744,321039, +chrY 22435610 22450036 uc004fuu.1 0 - 22435888 22448048 0 12 577,89,111,111,111,111,115,153,178,104,113,123, 0,988,1164,2196,2741,3293,4359,6484,8552,11749,12329,14303, +chrY 22435610 22450036 uc004fuv.1 0 - 22435888 22442218 0 11 577,89,111,111,111,111,115,153,104,113,123, 0,988,1164,2196,2741,3293,4359,6484,11749,12329,14303, +chrY 22459152 22473577 uc004fuw.1 0 - 22459430 22471589 0 12 577,89,111,111,111,111,115,153,178,104,113,123, 0,988,1163,2195,2740,3292,4358,6483,8551,11748,12328,14302, +chrY 22459152 22473577 uc004fux.1 0 - 22459430 22465759 0 11 577,89,111,111,111,111,115,153,104,113,123, 0,988,1163,2195,2740,3292,4358,6483,11748,12328,14302, +chrY 22627290 22651542 uc004fuy.1 0 - 22627857 22640374 0 5 826,116,121,87,88, 0,10324,13015,23976,24164, +chrY 22700521 22702366 uc004fuz.1 0 - 22700521 22700521 0 3 93,138,239, 0,311,1606, +chrY 22724076 22738477 uc004fva.1 0 - 22724354 22736504 0 12 577,89,111,111,111,111,115,153,178,104,113,108, 0,988,1163,2197,2742,3293,4359,6484,8552,11749,12319,14293, +chrY 22852332 22854411 uc004fvb.1 0 - 22852332 22852332 0 2 991,571, 0,1508, +chrY 22864393 22871740 uc004fvc.1 0 + 22866398 22870300 0 4 112,113,104,1713, 0,2001,2536,5634, +chrY 22864393 22973416 uc004fvd.1 0 + 22960982 22973138 0 12 112,113,104,178,153,115,111,111,111,111,89,577, 0,96585,97166,100293,102386,104549,105619,106170,106715,107749,107946,108446, +chrY 22959010 22973416 uc004fve.1 0 + 22960982 22973138 0 12 107,113,104,178,153,115,111,111,111,111,89,577, 0,1968,2549,5676,7769,9932,11002,11553,12098,13132,13329,13829, +chrY 22995127 22996972 uc004fvf.1 0 + 22995127 22995127 0 3 239,138,93, 0,1396,1752, +chrY 22995127 22996994 uc004fvg.1 0 - 22995127 22995127 0 4 239,99,138,115, 0,1187,1396,1752, +chrY 23045931 23070172 uc004fvh.1 0 + 23057099 23069605 0 5 88,87,121,116,826, 0,189,11116,13812,23415, +chrY 23407118 23408250 uc004fvi.1 0 + 23407118 23407118 0 2 60,106, 0,1026, +chrY 23539797 23560998 uc004fvj.1 0 + 23547878 23553803 0 9 31,123,137,119,118,106,125,125,320, 0,306,3494,8040,10218,13189,13987,20662,20881, +chrY 23684894 23696347 uc004fvk.1 0 - 23690744 23696301 0 5 1852,99,72,35,187, 0,5815,8850,10487,11266, +chrY 23684894 23735812 uc004fvl.1 0 - 23690744 23725624 0 20 1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52, 0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,50137,50366,50866, +chrY 23684894 23754545 uc004fvm.1 0 - 23690744 23754335 0 23 1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52,92,147,213, 0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,60985,61214,61714,62326,62692,69438, +chrY 23684894 23754545 uc004fvn.1 0 - 23690744 23754335 0 17 1852,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,213, 0,5815,10487,11266,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,69438, +chrY 23684894 23754545 uc004fvo.1 0 - 23690744 23754335 0 16 1852,99,35,72,72,72,72,72,72,72,140,64,52,92,147,213, 0,5815,10487,11266,13651,23437,28210,32989,35380,37825,39297,39526,40026,40638,41004,69438, +chrY 23715487 23754545 uc004fvp.1 0 - 23715487 23754335 0 20 72,72,72,72,140,64,52,92,147,140,64,52,92,147,140,64,52,92,147,213, 0,2396,4787,7232,8704,8933,9433,10045,10411,19544,19773,20273,20885,21251,30392,30621,31121,31733,32099,38845, +chrY 23775009 23846886 uc004fvq.1 0 + 23775275 23841036 0 24 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,31670,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvr.1 0 + 23775275 23841036 0 23 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvs.1 0 + 23775275 23841036 0 19 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,22131,26911,29288,34066,36443,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvt.1 0 + 23775275 23841036 0 17 269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvu.1 0 + 23775275 23841036 0 16 269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,19735,51001,55769,58153,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvv.1 0 + 23775275 23841036 0 25 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,48616,53385,55769,58153,60538,61354,65963,70025, +chrY 23775009 23846886 uc004fvw.1 0 + 23775275 23841036 0 21 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,60538,61354,65963,70025, +chrY 24237509 24250098 uc004fvx.1 0 - 24237541 24250062 0 3 291,116,105, 0,9782,12484, +chrY 24492261 24497157 uc004fvy.1 0 - 24492261 24492261 0 3 105,135,104, 0,2459,4792, +chrY 24600763 24603549 uc004fvz.1 0 - 24601138 24603223 0 2 448,1918, 0,868, +chrY 24601327 24603549 uc004fwa.1 0 - 24601600 24603223 0 1 2222, 0, +chrY 24735846 24735884 uc004fwb.1 0 - 24735846 24735846 0 1 38, 0, +chrY 24738968 24742766 uc004fwc.1 0 - 24742065 24742758 0 2 72,723, 0,3075, +chrY 24765501 24770366 uc004fwd.1 0 - 24765501 24765501 0 9 84,93,189,89,75,58,352,79,43, 0,166,348,792,1301,2732,3086,4557,4822, +chrY 24766145 24766176 uc004fwe.1 0 + 24766145 24766145 0 1 31, 0, +chrY 24832038 24832067 uc004fwf.1 0 + 24832038 24832038 0 1 29, 0, +chrY 25040866 25041998 uc004fwg.1 0 + 25040866 25040866 0 2 60,106, 0,1026, +chrY 25125736 25162560 uc004fwh.1 0 + 25125736 25125736 0 4 161,76,108,1001, 0,27167,29047,35823, +chrY 25173538 25194740 uc004fwi.1 0 + 25181619 25187545 0 9 31,123,137,119,118,106,125,125,320, 0,306,3494,8040,10218,13190,13988,20663,20882, +chrY 25318609 25330071 uc004fwj.1 0 - 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14018177 14100939 0 7 671,121,59,50,109,64,1157, 0,14691,18433,52715,73819,82952,83212, 1005 0.0119119581837 4 0 +chrY 14324840 14327296 uc004ftb.1 0 + 14325609 14326533 0 2 869,798, 0,1658, 769 0.313110749186 1 0 +chrY 14607045 14607786 uc004ftc.1 0 - 14607144 14607714 0 2 375,174, 0,567, 72 0.0971659919028 1 0 +chrY 14677491 14678232 uc004ftd.1 0 + 14677563 14678133 0 2 174,375, 0,366, 72 0.0971659919028 1 0 +chrY 15144025 15464921 uc004fte.1 0 + 15344422 15462536 0 6 190,60,153,186,790,3235, 0,196707,200365,301436,306978,317661, 2031 0.00632915337056 16 0 +chrY 15145019 15464921 uc004ftf.1 0 + 15451113 15462536 0 9 153,571,60,153,111,122,186,790,3235, 0,98275,195713,199371,224873,227935,300442,305984,316667, 1841 0.00575488743428 15 0 +chrY 15145019 15464921 uc004ftg.1 0 + 15243393 15462536 0 6 153,571,153,186,790,3235, 0,98275,199371,300442,305984,316667, 1841 0.00575488743428 15 0 +chrY 15145847 15464921 uc004fth.1 0 + 15243393 15462536 0 6 363,583,153,186,790,3235, 0,97435,198543,299614,305156,315839, 1688 0.00529030883118 13 0 +chrY 15243294 15354818 uc004fti.1 0 + 15243393 15354811 0 4 571,60,153,93, 0,97438,101096,111431, 784 0.00702987697715 7 1 +chrY 18196434 18200747 uc004ftj.1 0 - 18196434 18196434 0 3 207,118,158, 0,1542,4155, 483 0.111987015998 3 0 +chrY 18390253 18391834 uc004ftk.1 0 - 18390817 18391171 0 1 1581, 0, 663 0.41935483871 1 0 +chrY 18499533 18501494 uc004ftl.1 0 - 18499540 18501166 0 1 1961, 0, 328 0.167261601224 1 0 +chrY 18647060 18649021 uc004ftm.1 0 + 18647388 18649014 0 1 1961, 0, 328 0.167261601224 1 0 +chrY 18756722 18758303 uc004ftn.1 0 + 18757385 18757739 0 1 1581, 0, 663 0.41935483871 1 0 +chrY 18947806 18952124 uc004fto.1 0 + 18947806 18947806 0 3 158,118,207, 0,2658,4111, 0 0.0 0 0 +chrY 19167944 19169866 uc004ftp.1 0 + 19168061 19169745 0 2 630,814, 0,1108, 117 0.0608740894901 3 0 +chrY 19167944 19210237 uc004ftq.1 0 + 19168061 19172078 0 6 630,110,87,155,86,428, 0,3443,4112,5246,36002,41865, 1612 0.0381150545007 7 0 +chrY 19167944 19210237 uc004ftr.1 0 + 19168061 19209908 0 2 630,428, 0,41865, 1612 0.0381150545007 7 0 +chrY 19202479 19211795 uc004fts.1 0 - 19202479 19202479 0 5 1143,137,114,101,142, 0,6206,6925,7400,9174, 1637 0.175719192787 5 0 +chrY 19351155 19360471 uc004ftt.1 0 + 19351155 19351155 0 5 142,101,114,137,1143, 0,1815,2277,2973,8173, 0 0.0 0 0 +chrY 19352713 19395009 uc004ftu.1 0 - 19390871 19394892 0 6 428,86,155,87,110,630, 0,6205,36891,38093,38743,41666, 117 0.0027662190278 3 0 +chrY 19352713 19395009 uc004ftv.1 0 - 19353042 19394892 0 2 428,630, 0,41666, 117 0.0027662190278 3 0 +chrY 19393087 19395009 uc004ftw.1 0 - 19393208 19394892 0 2 814,630, 0,1292, 117 0.0608740894901 3 0 +chrY 19493774 19499502 uc004ftx.1 0 - 19493774 19493774 0 2 334,1161, 0,4567, 1495 0.260998603352 2 0 +chrY 19553972 19698690 uc004fty.1 0 - 19553972 19553972 0 2 143,372, 0,144346, 625 0.00431874404013 3 0 +chrY 19611913 19614093 uc004ftz.1 0 - 19613740 19613983 0 1 2180, 0, 110 0.0504587155963 1 0 +chrY 20076704 20124427 uc004fua.1 0 - 20076704 20076704 0 9 1434,156,78,122,919,240,264,126,122, 0,3493,3858,9675,11025,18474,19209,24738,47601, 3668 0.0768602141525 20 0 +chrY 20076704 20124427 uc004fub.1 0 - 20076704 20076704 0 11 1434,61,156,78,146,122,919,240,264,126,122, 0,1626,3493,3858,4528,9675,11025,18474,19209,24738,47601, 3668 0.0768602141525 20 0 +chrY 20188623 20211564 uc004fuc.1 0 + 20208498 20209756 0 4 221,298,1243,208, 0,19860,21020,22733, 236 0.0102872586199 4 0 +chrY 20188655 20211564 uc004fud.1 0 + 20208498 20211377 0 4 101,298,92,208, 0,19828,22139,22701, 204 0.00890479724126 3 1 +chrY 20213723 20225769 uc004fue.1 0 + 20218906 20225394 0 5 365,4267,93,96,699, 0,949,7289,9766,11347, 4599 0.38178648514 2 0 +chrY 20326688 20337013 uc004fuf.1 0 - 20327268 20336982 0 11 931,200,70,600,138,180,139,128,97,148,125, 0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200, 31 0.00300242130751 1 0 +chrY 20326688 20366212 uc004fug.1 0 - 20327268 20365808 0 27 931,200,70,600,138,180,139,359,97,148,125,182,195,120,163,182,159,120,159,146,130,135,171,123,78,169,268, 0,1026,1379,1732,2519,2829,3460,4036,4961,9937,10200,10408,10864,11181,15457,15715,26357,26631,27169,29937,30206,34113,35903,36320,37747,38970,39256, 318 0.00804574435786 5 0 +chrY 20342403 20366212 uc004fuh.1 0 - 20342405 20365808 0 11 182,159,120,159,146,130,171,123,78,169,268, 0,10642,10916,11454,14222,14491,20188,20605,22032,23255,23541, 287 0.0120542651938 4 0 +chrY 21021299 21023423 uc004fui.1 0 - 21021299 21021299 0 1 2124, 0, 2124 1.0 1 0 +chrY 21036941 21090502 uc004fuj.1 0 - 21036941 21036941 0 6 155,240,60,110,105,958, 0,760,2521,4204,41684,52603, 1628 0.0303952502754 6 0 +chrY 21146998 21164428 uc004fuk.1 0 + 21147145 21163620 0 7 163,84,104,51,82,92,814, 0,3883,6865,8749,12299,13759,16616, 147 0.00843373493976 2 0 +chrY 21146998 21164428 uc004ful.1 0 + 21147145 21163620 0 6 163,84,104,82,92,814, 0,3883,6865,12299,13759,16616, 147 0.00843373493976 2 0 +chrY 21327341 21352306 uc004fum.1 0 + 21327437 21352306 0 7 99,78,181,98,172,158,102, 0,710,3800,5216,12737,23441,24863, 96 0.00384538353695 1 0 +chrY 21966421 21972836 uc004fun.1 0 - 21966473 21972204 0 5 144,89,111,104,86, 0,552,723,5775,6329, 182 0.028371005456 2 0 +chrY 22082636 22097060 uc004fuo.1 0 + 22084624 22096782 0 12 123,113,104,178,153,115,111,111,111,111,89,577, 0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13347,13847, 369 0.0255823627288 6 0 +chrY 22082636 22097060 uc004fup.1 0 + 22090452 22096782 0 11 123,113,104,153,115,111,111,111,111,89,577, 0,1984,2571,7787,9950,11020,11572,12117,13149,13347,13847, 369 0.0255823627288 6 0 +chrY 22106177 22120600 uc004fuq.1 0 + 22108165 22120322 0 12 123,113,104,178,153,115,111,111,111,111,89,577, 0,1984,2571,5694,7787,9950,11020,11572,12117,13149,13346,13846, 369 0.0255841364487 6 0 +chrY 22106177 22120600 uc004fur.1 0 + 22113993 22120322 0 11 123,113,104,153,115,111,111,111,111,89,577, 0,1984,2571,7787,9950,11020,11572,12117,13149,13346,13846, 369 0.0255841364487 6 0 +chrY 22154873 22165940 uc004fus.1 0 - 22154873 22154873 0 6 63,92,162,99,162,81, 0,1183,3901,5672,6366,10986, 659 0.0595463992048 6 0 +chrY 22381088 22702366 uc004fut.1 0 + 22381088 22381088 0 4 25,114,138,239, 0,319412,319744,321039, 1435 0.00446653676878 18 0 +chrY 22435610 22450036 uc004fuu.1 0 - 22435888 22448048 0 12 577,89,111,111,111,111,115,153,178,104,113,123, 0,988,1164,2196,2741,3293,4359,6484,8552,11749,12329,14303, 369 0.0255788160266 6 0 +chrY 22435610 22450036 uc004fuv.1 0 - 22435888 22442218 0 11 577,89,111,111,111,111,115,153,104,113,123, 0,988,1164,2196,2741,3293,4359,6484,11749,12329,14303, 369 0.0255788160266 6 0 +chrY 22459152 22473577 uc004fuw.1 0 - 22459430 22471589 0 12 577,89,111,111,111,111,115,153,178,104,113,123, 0,988,1163,2195,2740,3292,4358,6483,8551,11748,12328,14302, 369 0.0255805892548 6 0 +chrY 22459152 22473577 uc004fux.1 0 - 22459430 22465759 0 11 577,89,111,111,111,111,115,153,104,113,123, 0,988,1163,2195,2740,3292,4358,6483,11748,12328,14302, 369 0.0255805892548 6 0 +chrY 22627290 22651542 uc004fuy.1 0 - 22627857 22640374 0 5 826,116,121,87,88, 0,10324,13015,23976,24164, 227 0.00936005277915 3 0 +chrY 22700521 22702366 uc004fuz.1 0 - 22700521 22700521 0 3 93,138,239, 0,311,1606, 470 0.254742547425 3 0 +chrY 22724076 22738477 uc004fva.1 0 - 22724354 22736504 0 12 577,89,111,111,111,111,115,153,178,104,113,108, 0,988,1163,2197,2742,3293,4359,6484,8552,11749,12319,14293, 112 0.00777723769183 2 0 +chrY 22852332 22854411 uc004fvb.1 0 - 22852332 22852332 0 2 991,571, 0,1508, 1562 0.751322751323 2 0 +chrY 22864393 22871740 uc004fvc.1 0 + 22866398 22870300 0 4 112,113,104,1713, 0,2001,2536,5634, 116 0.0157887573159 3 0 +chrY 22864393 22973416 uc004fvd.1 0 + 22960982 22973138 0 12 112,113,104,178,153,115,111,111,111,111,89,577, 0,96585,97166,100293,102386,104549,105619,106170,106715,107749,107946,108446, 227 0.00208212945892 6 0 +chrY 22959010 22973416 uc004fve.1 0 + 22960982 22973138 0 12 107,113,104,178,153,115,111,111,111,111,89,577, 0,1968,2549,5676,7769,9932,11002,11553,12098,13132,13329,13829, 111 0.00770512286547 3 0 +chrY 22995127 22996972 uc004fvf.1 0 + 22995127 22995127 0 3 239,138,93, 0,1396,1752, 569 0.308401084011 3 1 +chrY 22995127 22996994 uc004fvg.1 0 - 22995127 22995127 0 4 239,99,138,115, 0,1187,1396,1752, 591 0.316550615961 4 0 +chrY 23045931 23070172 uc004fvh.1 0 + 23057099 23069605 0 5 88,87,121,116,826, 0,189,11116,13812,23415, 227 0.00936430015263 3 0 +chrY 23407118 23408250 uc004fvi.1 0 + 23407118 23407118 0 2 60,106, 0,1026, 0 0.0 0 0 +chrY 23539797 23560998 uc004fvj.1 0 + 23547878 23553803 0 9 31,123,137,119,118,106,125,125,320, 0,306,3494,8040,10218,13189,13987,20662,20881, 332 0.0156596386963 4 0 +chrY 23684894 23696347 uc004fvk.1 0 - 23690744 23696301 0 5 1852,99,72,35,187, 0,5815,8850,10487,11266, 46 0.00401641491312 1 0 +chrY 23684894 23735812 uc004fvl.1 0 - 23690744 23725624 0 20 1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52, 0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,50137,50366,50866, 449 0.0088180996897 5 0 +chrY 23684894 23754545 uc004fvm.1 0 - 23690744 23754335 0 23 1852,99,35,72,72,72,72,72,72,72,72,72,140,64,52,92,147,140,64,52,92,147,213, 0,5815,10487,11266,13651,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,60985,61214,61714,62326,62692,69438, 659 0.0094614578398 9 0 +chrY 23684894 23754545 uc004fvn.1 0 - 23690744 23754335 0 17 1852,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,213, 0,5815,10487,11266,23437,25814,28210,30593,32989,35380,37825,39297,39526,40026,40638,41004,69438, 659 0.0094614578398 9 0 +chrY 23684894 23754545 uc004fvo.1 0 - 23690744 23754335 0 16 1852,99,35,72,72,72,72,72,72,72,140,64,52,92,147,213, 0,5815,10487,11266,13651,23437,28210,32989,35380,37825,39297,39526,40026,40638,41004,69438, 659 0.0094614578398 9 0 +chrY 23715487 23754545 uc004fvp.1 0 - 23715487 23754335 0 20 72,72,72,72,140,64,52,92,147,140,64,52,92,147,140,64,52,92,147,213, 0,2396,4787,7232,8704,8933,9433,10045,10411,19544,19773,20273,20885,21251,30392,30621,31121,31733,32099,38845, 613 0.0156946080188 8 0 +chrY 23775009 23846886 uc004fvq.1 0 + 23775275 23841036 0 24 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,31670,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvr.1 0 + 23775275 23841036 0 23 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,46232,48616,51001,53385,55769,58153,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvs.1 0 + 23775275 23841036 0 19 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,22131,26911,29288,34066,36443,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvt.1 0 + 23775275 23841036 0 17 269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,22131,24515,26911,29288,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvu.1 0 + 23775275 23841036 0 16 269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,19735,51001,55769,58153,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvv.1 0 + 23775275 23841036 0 25 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,48616,53385,55769,58153,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 23775009 23846886 uc004fvw.1 0 + 23775275 23841036 0 21 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6869,7290,7942,8430,8583,10123,12566,14957,17353,19735,22131,24515,26911,29288,34066,36443,60538,61354,65963,70025, 266 0.00370076658736 7 0 +chrY 24237509 24250098 uc004fvx.1 0 - 24237541 24250062 0 3 291,116,105, 0,9782,12484, 36 0.0028596393677 1 0 +chrY 24492261 24497157 uc004fvy.1 0 - 24492261 24492261 0 3 105,135,104, 0,2459,4792, 344 0.0702614379085 3 0 +chrY 24600763 24603549 uc004fvz.1 0 - 24601138 24603223 0 2 448,1918, 0,868, 326 0.117013639627 2 0 +chrY 24601327 24603549 uc004fwa.1 0 - 24601600 24603223 0 1 2222, 0, 326 0.146714671467 2 0 +chrY 24735846 24735884 uc004fwb.1 0 - 24735846 24735846 0 1 38, 0, 38 1.0 1 0 +chrY 24738968 24742766 uc004fwc.1 0 - 24742065 24742758 0 2 72,723, 0,3075, 8 0.00210637177462 1 0 +chrY 24765501 24770366 uc004fwd.1 0 - 24765501 24765501 0 9 84,93,189,89,75,58,352,79,43, 0,166,348,792,1301,2732,3086,4557,4822, 1062 0.21829393628 9 0 +chrY 24766145 24766176 uc004fwe.1 0 + 24766145 24766145 0 1 31, 0, 0 0.0 0 0 +chrY 24832038 24832067 uc004fwf.1 0 + 24832038 24832038 0 1 29, 0, 0 0.0 0 0 +chrY 25040866 25041998 uc004fwg.1 0 + 25040866 25040866 0 2 60,106, 0,1026, 0 0.0 0 0 +chrY 25125736 25162560 uc004fwh.1 0 + 25125736 25125736 0 4 161,76,108,1001, 0,27167,29047,35823, 0 0.0 0 0 +chrY 25173538 25194740 uc004fwi.1 0 + 25181619 25187545 0 9 31,123,137,119,118,106,125,125,320, 0,306,3494,8040,10218,13190,13988,20663,20882, 332 0.0156589001038 4 0 +chrY 25318609 25330071 uc004fwj.1 0 - 25324468 25330025 0 5 1851,99,72,35,187, 0,5824,8858,10495,11275, 46 0.00401326121096 1 0 +chrY 25318609 25368905 uc004fwk.1 0 - 25324468 25368720 0 19 1851,99,35,72,72,72,72,72,72,72,72,72,72,140,64,52,92,147,188, 0,5824,10495,11275,21062,23439,25819,28196,30575,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108, 231 0.00459281056148 3 0 +chrY 25318609 25368905 uc004fwl.1 0 - 25324468 25368720 0 17 1851,99,35,72,72,72,72,72,72,72,72,140,64,52,92,147,188, 0,5824,10495,11275,21062,23439,25819,32952,35348,37738,40181,41653,41882,42382,42994,43360,50108, 231 0.00459281056148 3 0 +chrY 25389395 25462570 uc004fwm.1 0 + 25389661 25456710 0 23 269,147,92,52,64,140,147,92,52,64,140,72,72,72,72,72,72,72,72,72,35,99,1852, 0,6870,7291,7943,8431,8584,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,59442,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25389395 25462570 uc004fwn.1 0 + 25389661 25456710 0 23 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25389395 25462570 uc004fwo.1 0 + 25389661 25456710 0 19 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25389395 25462570 uc004fwp.1 0 + 25389661 25456710 0 17 269,147,92,52,64,140,72,72,72,72,72,72,72,72,35,99,1852, 0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,37738,40115,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25389395 25462570 uc004fwq.1 0 + 25389661 25456710 0 16 269,147,92,52,64,140,72,72,72,72,72,72,72,35,99,1852, 0,17718,18139,18791,19279,19432,20972,23415,30585,54673,57057,59442,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25389395 25462570 uc004fwr.1 0 + 25389661 25456710 0 24 269,147,92,52,64,140,72,72,72,72,72,72,72,72,72,72,72,72,72,72,72,35,99,1852, 0,17718,18139,18791,19279,19432,20972,23415,25805,28201,30585,32981,35358,37738,40115,49903,52288,54673,57057,59442,61827,62644,67251,71323, 266 0.00363512128459 6 0 +chrY 25586437 25607639 uc004fws.1 0 - 25593632 25599558 0 9 320,125,125,106,118,119,137,123,31, 0,414,7089,7906,10866,13043,17571,20773,21171, 332 0.0156589001038 4 0 +chrY 25739177 25740308 uc004fwt.1 0 - 25739177 25739177 0 2 106,60, 0,1071, 166 0.146772767462 2 0 +chrY 25949150 25949179 uc004fwu.1 0 - 25949150 25949150 0 1 29, 0, 29 1.0 1 0 +chrY 26010845 26015710 uc004fwv.1 0 + 26010845 26010845 0 9 43,79,350,58,75,89,189,93,84, 0,229,1427,2075,3489,3984,4328,4606,4781, 68 0.013977389517 2 0 +chrY 26012853 26012887 uc004fww.1 0 - 26012853 26012853 0 1 34, 0, 34 1.0 1 0 +chrY 26015032 26015066 uc004fwx.1 0 - 26015032 26015032 0 1 34, 0, 34 1.0 1 0 +chrY 26015781 26015809 uc004fwy.1 0 - 26015781 26015781 0 1 28, 0, 28 1.0 1 0 +chrY 26016791 26016820 uc004fwz.1 0 - 26016791 26016791 0 1 29, 0, 29 1.0 1 0 +chrY 26033830 26033856 uc004fxa.1 0 + 26033830 26033830 0 1 26, 0, 0 0.0 0 0 +chrY 26033938 26033965 uc004fxb.1 0 + 26033938 26033938 0 1 27, 0, 0 0.0 0 0 +chrY 26038442 26042240 uc004fxc.1 0 + 26038450 26039143 0 2 723,72, 0,3726, 8 0.00210637177462 1 0 +chrY 26045324 26045355 uc004fxd.1 0 + 26045324 26045324 0 1 31, 0, 0 0.0 0 0 +chrY 26177651 26179873 uc004fxe.1 0 + 26177977 26179600 0 1 2222, 0, 326 0.146714671467 2 0 +chrY 26177651 26180436 uc004fxf.1 0 + 26177977 26180062 0 2 1918,447, 0,2338, 326 0.117055655296 2 0 +chrY 26284024 26288923 uc004fxg.1 0 + 26284024 26284024 0 3 104,135,105, 0,2302,4794, 0 0.0 0 0 +chrY 26531047 26543636 uc004fxh.1 0 + 26531083 26543604 0 3 105,116,291, 0,2691,12298, 36 0.0028596393677 1 0 +chrY 57509844 57524511 uc004fxi.1 0 + 57515927 57516794 0 2 348,8690, 0,5977, 454 0.0309538419581 2 0 +chrY 57623412 57685814 uc004fxj.1 0 + 57631523 57684009 0 8 93,155,58,138,91,68,93,1874, 0,8102,14267,16757,19142,38458,58346,60528, 102 0.00163456299478 6 0 +chrY 57623412 57685814 uc004fxk.1 0 + 57631523 57684197 0 7 93,155,58,138,91,93,1874, 0,8102,14267,16757,19142,58346,60528, 102 0.00163456299478 6 0 +chrY 57623412 57685814 uc004fxl.1 0 + 57631523 57684009 0 7 93,90,138,91,68,93,1874, 0,8102,16757,19142,38458,58346,60528, 102 0.00163456299478 6 0 +chrY 57739639 57752876 uc004fxm.1 0 + 57739832 57751911 0 9 207,101,138,112,172,117,202,106,1002, 0,3827,5301,5868,6103,6868,7697,8502,12235, 193 0.014580342978 2 0 +chrY 57739639 57752876 uc004fxn.1 0 + 57739818 57752468 0 9 207,114,112,179,146,202,106,85,1002, 0,5325,5868,6096,6839,7697,8502,9942,12235, 193 0.014580342978 2 0 +chrY 57762360 57765519 uc004fxo.1 0 + 57763019 57765518 0 7 847,112,147,137,136,202,159, 0,1379,1697,2021,2397,2710,3000, 1113 0.35232668566 5 0 +chrY 57763739 57767724 uc004fxp.1 0 + 57764815 57767433 0 9 112,147,137,136,202,159,153,69,425, 0,318,642,1018,1331,1621,2439,3351,3560, 454 0.113927227102 4 0 diff -r 000000000000 -r 56dab41a4c5f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 01 09:12:47 2014 -0400 @@ -0,0 +1,9 @@ + + + + + + + + +