BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237567.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,442,790 number of mapped reads = 2,817,344 (81.83%) number of supplementary alignments = 20,647 (0.6%) number of secondary alignments = 0 number of mapped bases = 173,944,664 bp number of sequenced bases = 173,849,662 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,627 duplication rate = 5.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3871 >>>>>>> ACTG content number of A's = 46,921,722 bp (26.99%) number of C's = 29,594,044 bp (17.02%) number of T's = 56,268,151 bp (32.37%) number of G's = 40,785,592 bp (23.46%) number of N's = 280,153 bp (0.16%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,591,895 number of insertions = 14,696 mapped reads with insertion percentage = 0.52% number of deletions = 59,415 mapped reads with deletion percentage = 2.08% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.4962X There is a 4.48% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 15273626 0.061278186344017174 0.7242267504236812 chr2 243199373 15561257 0.06398559670628756 0.6235358710348415 chr3 198022430 13562803 0.06849124616842647 0.3347336064568127 chr4 191154276 11090234 0.0580171902615456 0.3133775802513313 chr5 180915260 8959565 0.049523544890574735 0.2856873164114047 chr6 171115067 10112078 0.059095193528457664 0.39168497171131333 chr7 159138663 11311564 0.07107992355069616 0.7702564468660303 chr8 146364022 7755284 0.05298627281505013 0.9536527444188809 chr9 141213431 5596498 0.03963148519491747 0.40941345719774663 chr10 135534747 9297032 0.06859519205064071 0.4370728208258717 chr11 135006516 7628079 0.056501561746841907 0.42737888776129773 chr12 133851895 9037979 0.06752223418278837 0.33770355048020756 chr13 115169878 8216441 0.07134192674928422 0.33355547358458554 chr14 107349540 4905964 0.04570083858766419 0.30278775153136894 chr15 102531392 5759120 0.05616933397334545 0.31276208814822926 chr16 90354753 3207448 0.0354983871186057 0.2723851462317389 chr17 81195210 3028853 0.03730334585008155 0.2713076195154065 chr18 78077248 4343435 0.055629970462073665 0.719796235079217 chr19 59128983 2330505 0.03941391990455848 0.5093046651019929 chr20 63025520 2905612 0.04610215036702593 0.29391857617183564 chr21 48129895 2047007 0.042530884391083754 0.2822280330942924 chr22 51304566 1250135 0.0243669345141717 0.1957791434038135 chrMT 16571 115990 6.999577575282119 5.584965434050183 chrX 155270560 10153487 0.0653922224535031 0.3774093069205996 chrY 59373566 494668 0.008331451744030332 0.15953792899552185