BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525231.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 451,742 number of mapped reads = 415,793 (92.04%) number of supplementary alignments = 1,467 (0.32%) number of secondary alignments = 0 number of mapped bases = 25,722,969 bp number of sequenced bases = 25,714,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,091 duplication rate = 1.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4846 >>>>>>> ACTG content number of A's = 6,998,660 bp (27.22%) number of C's = 5,352,415 bp (20.82%) number of T's = 7,599,872 bp (29.56%) number of G's = 5,762,533 bp (22.41%) number of N's = 695 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 123,298 number of insertions = 2,050 mapped reads with insertion percentage = 0.49% number of deletions = 5,219 mapped reads with deletion percentage = 1.24% homopolymer indels = 43.22% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 0.109X There is a 0.79% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2046065 0.00820886620779974 0.16055668387241842 chr2 243199373 2160104 0.008882029477929616 0.11897359576017465 chr3 198022430 1713609 0.008653610603606874 0.09519628659829489 chr4 191154276 1643303 0.00859673680540633 0.09807101614896795 chr5 180915260 1537237 0.00849700019777215 0.09449671273240236 chr6 171115067 1483211 0.008667915841683305 0.09857526085362353 chr7 159138663 1410350 0.008862396939956697 0.13073614453887386 chr8 146364022 1314385 0.008980246525338038 0.10637278805358942 chr9 141213431 1077478 0.0076301382408872995 0.09673782181682704 chr10 135534747 1266577 0.009345035336215295 0.1188857176500099 chr11 135006516 1168232 0.008653152711532826 0.1008585806818494 chr12 133851895 1168611 0.008730627235423153 0.09599635483522177 chr13 115169878 806890 0.007006085393265763 0.08604984273186173 chr14 107349540 790417 0.007363021769818482 0.08943215066695889 chr15 102531392 725289 0.007073823790473849 0.08624339361327289 chr16 90354753 778520 0.008616259512103364 0.09915122755072475 chr17 81195210 711302 0.008760393624205172 0.0975460379876145 chr18 78077248 677100 0.0086721806588265 0.1464746066860273 chr19 59128983 532308 0.0090024886780143 0.1264568421112997 chr20 63025520 559489 0.008877181814604623 0.09758898954075552 chr21 48129895 336552 0.0069925770667066695 0.08939626734080999 chr22 51304566 324890 0.006332574765372735 0.08168059441872418 chrMT 16571 3329 0.2008931265463762 0.44559320333916114 chrX 155270560 1406022 0.009055303207510811 0.09967561751182816 chrY 59373566 81699 0.0013760163908632336 0.05459963989087014