BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716689.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 = 927,384 number of mapped reads = 853,426 (92.03%) number of supplementary alignments = 3,519 (0.38%) number of secondary alignments = 0 number of mapped bases = 49,269,063 bp number of sequenced bases = 49,253,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,431 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7624 >>>>>>> ACTG content number of A's = 11,592,097 bp (23.54%) number of C's = 9,993,433 bp (20.29%) number of T's = 15,932,110 bp (32.35%) number of G's = 11,734,769 bp (23.83%) number of N's = 972 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 252,195 number of insertions = 3,818 mapped reads with insertion percentage = 0.44% number of deletions = 9,679 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0159X std coverageData = 0.1791X There is a 1.46% of reference with a coverageData >= 1X There is a 0.09% 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 3997893 0.01603965111083916 0.2614140178163377 chr2 243199373 4185556 0.017210389765272956 0.25231379212197075 chr3 198022430 3221974 0.01627075276270471 0.13682033537005894 chr4 191154276 3170093 0.01658395023295215 0.1590620738439942 chr5 180915260 2902908 0.01604567795994655 0.13559197668593218 chr6 171115067 2784449 0.016272377697751188 0.1462171804090387 chr7 159138663 2685127 0.016872876454919066 0.19289793611067213 chr8 146364022 2513326 0.017171747302762698 0.22116680632685787 chr9 141213431 2071093 0.014666402376414181 0.15035201967850959 chr10 135534747 2427559 0.017910971568051107 0.20481563017889495 chr11 135006516 2258535 0.016729081431891776 0.16014084769057882 chr12 133851895 2206517 0.01648476474688685 0.13874824793051665 chr13 115169878 1526133 0.013251147144568478 0.12271229795450726 chr14 107349540 1511462 0.01407981813429289 0.12818667011583343 chr15 102531392 1422742 0.01387615999595519 0.12630305046565207 chr16 90354753 1450966 0.016058546471816485 0.14379038169341468 chr17 81195210 1408023 0.017341207689468383 0.14698396610626235 chr18 78077248 1248000 0.015984169933858323 0.22105782156798093 chr19 59128983 1076655 0.018208583090292624 0.21662867195036872 chr20 63025520 1062055 0.016851189803749337 0.14354613512385797 chr21 48129895 647439 0.013451909670694274 0.14822843827938498 chr22 51304566 603884 0.011770570284134165 0.11630896553883954 chrMT 16571 7971 0.48102106088950575 0.7340418256699083 chrX 155270560 2681183 0.017267813035516843 0.14612467521611952 chrY 59373566 197520 0.0033267329774330887 0.16023118622170385