BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716345.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 = 976,535 number of mapped reads = 897,528 (91.91%) number of supplementary alignments = 19,830 (2.03%) number of secondary alignments = 0 number of mapped bases = 70,824,718 bp number of sequenced bases = 70,790,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,536 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0901 >>>>>>> ACTG content number of A's = 18,358,605 bp (25.93%) number of C's = 13,696,943 bp (19.35%) number of T's = 21,924,702 bp (30.97%) number of G's = 16,805,216 bp (23.74%) number of N's = 5,035 bp (0.01%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 458,860 number of insertions = 6,141 mapped reads with insertion percentage = 0.67% number of deletions = 17,989 mapped reads with deletion percentage = 1.97% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.2539X There is a 2.09% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7120372 0.028567118394461292 0.5336588197656135 chr2 243199373 5936112 0.024408418191111045 0.2500328114034245 chr3 198022430 4649399 0.023479153346416363 0.1627557158115424 chr4 191154276 4602542 0.024077630363863792 0.18578958673464888 chr5 180915260 4269232 0.02359796514677645 0.16353250392780402 chr6 171115067 4003353 0.023395677950440216 0.17209596025373752 chr7 159138663 3830826 0.02407225200830046 0.28834509931691965 chr8 146364022 1959093 0.013385072186660735 0.24779666916762513 chr9 141213431 2928108 0.020735336428444967 0.21143803172494033 chr10 135534747 3392046 0.02502713197229047 0.2466371808517608 chr11 135006516 4033549 0.02987669869208387 0.26639196697590317 chr12 133851895 3126487 0.023357809017197702 0.1621828775280659 chr13 115169878 2559271 0.02222170453284669 0.15871353616600944 chr14 107349540 2073671 0.01931699940213996 0.15435954968672602 chr15 102531392 2023726 0.019737623380749577 0.148412175886662 chr16 90354753 1591654 0.017615608998455233 0.1522136259675583 chr17 81195210 2149015 0.02646726327821555 0.19197545443829286 chr18 78077248 1857338 0.023788466519721597 0.3346696895032321 chr19 59128983 1354065 0.022900190926672965 0.40207580611463034 chr20 63025520 1475242 0.023407057966360292 0.16585540166181992 chr21 48129895 924087 0.019199854892681566 0.16355684591186853 chr22 51304566 794860 0.015492968013802124 0.13183220747256533 chrMT 16571 1795 0.1083217669422485 0.36830062260793667 chrX 155270560 3959270 0.025499167388846927 0.19320371976371353 chrY 59373566 209605 0.003530274735393188 0.12455203584088549