BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716501.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 = 727,997 number of mapped reads = 644,790 (88.57%) number of supplementary alignments = 2,262 (0.31%) number of secondary alignments = 0 number of mapped bases = 37,249,553 bp number of sequenced bases = 37,237,269 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,569 duplication rate = 1.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1796 >>>>>>> ACTG content number of A's = 9,537,677 bp (25.61%) number of C's = 7,162,916 bp (19.24%) number of T's = 11,844,809 bp (31.81%) number of G's = 8,691,519 bp (23.34%) number of N's = 348 bp (0%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 192,288 number of insertions = 2,544 mapped reads with insertion percentage = 0.39% number of deletions = 7,503 mapped reads with deletion percentage = 1.16% homopolymer indels = 40.21% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.132X There is a 1.13% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 2936496 0.011781298631147644 0.14623748781019397 chr2 243199373 3119169 0.01282556349353746 0.16960389309362042 chr3 198022430 2470687 0.012476803764098845 0.11823207982838703 chr4 191154276 2421755 0.012669112356136884 0.1279781024341726 chr5 180915260 2210535 0.012218621027325169 0.11468495995553916 chr6 171115067 2148533 0.012556071406616695 0.12324256592932518 chr7 159138663 2005378 0.01260145059783492 0.15131664682284862 chr8 146364022 1831310 0.012512022934160691 0.1388951089114494 chr9 141213431 1614126 0.01143039998794449 0.12114558593472084 chr10 135534747 1840526 0.013579735386970545 0.1655818707910123 chr11 135006516 1671697 0.01238234308631444 0.12592469222622965 chr12 133851895 1678789 0.012542138458331128 0.1169372501764471 chr13 115169878 1168375 0.010144796714988271 0.10500350351168548 chr14 107349540 1134618 0.010569379244661878 0.11008476264889772 chr15 102531392 1096129 0.010690667303141657 0.10851617025527768 chr16 90354753 1110930 0.012295202666316845 0.12033304436419423 chr17 81195210 1055870 0.013004092236475527 0.12183301366356042 chr18 78077248 975246 0.012490783486631086 0.16471785579617182 chr19 59128983 814133 0.013768763788817405 0.1465215752804705 chr20 63025520 798114 0.012663346530103996 0.11859193509305485 chr21 48129895 484350 0.010063391993687084 0.11451794780097191 chr22 51304566 451604 0.008802413414821597 0.0981831099028753 chrMT 16571 6074 0.3665439623438537 0.6469086577311813 chrX 155270560 2077668 0.013380952577230352 0.12432626630852193 chrY 59373566 127441 0.0021464265764330206 0.07888738794703766