BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238032.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 = 2,780,741 number of mapped reads = 2,520,297 (90.63%) number of supplementary alignments = 21,874 (0.79%) number of secondary alignments = 0 number of mapped bases = 170,118,283 bp number of sequenced bases = 170,046,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,352 duplication rate = 5.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8938 >>>>>>> ACTG content number of A's = 46,276,052 bp (27.21%) number of C's = 33,053,483 bp (19.44%) number of T's = 52,234,605 bp (30.72%) number of G's = 38,457,369 bp (22.62%) number of N's = 24,690 bp (0.01%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,193,134 number of insertions = 10,923 mapped reads with insertion percentage = 0.43% number of deletions = 40,535 mapped reads with deletion percentage = 1.59% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.055X std coverageData = 0.4868X There is a 3.84% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% 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% 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 15362064 0.06163300190935131 1.0830175650841527 chr2 243199373 2232322 0.00917897925666116 0.38951142765674024 chr3 198022430 4869049 0.02458837112543261 0.2080174985983906 chr4 191154276 12074898 0.06316833843675043 0.34126651927977475 chr5 180915260 23081257 0.12758048712972028 0.4875339082940804 chr6 171115067 1591014 0.009297918809218594 0.15662320319323744 chr7 159138663 7284192 0.0457726102675627 0.5357309927386634 chr8 146364022 3585495 0.02449710626290387 0.2830209018299685 chr9 141213431 1300659 0.009210589890702394 0.23376242360438163 chr10 135534747 8859537 0.06536727441561535 0.5003759904895194 chr11 135006516 10547741 0.07812764385387147 0.4818908593754767 chr12 133851895 14112339 0.10543249312981337 0.44512043368095333 chr13 115169878 876170 0.00760763157185944 0.11396857669845538 chr14 107349540 6011200 0.055996513818317245 0.32006445131326855 chr15 102531392 4092078 0.0399104890724589 0.2668628274841372 chr16 90354753 9345307 0.10342905812602908 0.4439557091480568 chr17 81195210 2581337 0.03179173993145655 0.259645578268955 chr18 78077248 8028628 0.10282929029465793 0.535460629557883 chr19 59128983 6697912 0.11327629294757192 0.8073080799157559 chr20 63025520 3447996 0.05470793418285164 0.3176323822724665 chr21 48129895 1766997 0.036713086533847625 0.26290888242026605 chr22 51304566 360329 0.0070233319973898615 0.10563814693630331 chrMT 16571 78551 4.740269144891678 3.9067283614929083 chrX 155270560 21474303 0.13830247665751963 0.5594117578345003 chrY 59373566 456908 0.007695478489535225 0.11210358352311767