BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716498.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 = 2,661,860 number of mapped reads = 2,242,787 (84.26%) number of supplementary alignments = 11,633 (0.44%) number of secondary alignments = 0 number of mapped bases = 129,323,537 bp number of sequenced bases = 129,289,381 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,312 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8359 >>>>>>> ACTG content number of A's = 34,169,407 bp (26.43%) number of C's = 22,858,597 bp (17.68%) number of T's = 40,747,818 bp (31.52%) number of G's = 31,509,811 bp (24.37%) number of N's = 3,748 bp (0%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 623,139 number of insertions = 9,328 mapped reads with insertion percentage = 0.41% number of deletions = 21,794 mapped reads with deletion percentage = 0.97% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.3491X There is a 3.64% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 14154221 0.05678710425359382 0.6309671977674275 chr2 243199373 11376441 0.04677824971201714 0.47260101949053224 chr3 198022430 11651527 0.058839430462498614 0.2756450900520648 chr4 191154276 5830816 0.030503194184366558 0.20773541339211374 chr5 180915260 5738224 0.0317177445396259 0.20352826200470364 chr6 171115067 9527353 0.05567804850288256 0.36225314235588546 chr7 159138663 7657365 0.04811756524559968 0.41214376923837903 chr8 146364022 8733873 0.05967226700015117 0.3098262785009925 chr9 141213431 4743705 0.03359244914883486 0.2868217162027582 chr10 135534747 6583987 0.04857785288078193 0.4245714558704624 chr11 135006516 4211117 0.031191953727626006 0.27171951533175387 chr12 133851895 5851651 0.043717356410979465 0.24113768647605688 chr13 115169878 2981466 0.025887550215169978 0.18168567645724684 chr14 107349540 2911021 0.02711721913293713 0.2081337260746715 chr15 102531392 3943710 0.038463439567854495 0.22372472239824306 chr16 90354753 2694250 0.029818575233114743 0.23432317769850974 chr17 81195210 2885645 0.03553959648604887 0.22400949363497386 chr18 78077248 2475230 0.03170232127033985 0.5117671901810192 chr19 59128983 2795585 0.04727943654975429 0.4533251808814952 chr20 63025520 1951371 0.03096160095148759 0.20019770731186895 chr21 48129895 1230769 0.025571819759839493 0.19997379614502492 chr22 51304566 2040741 0.03977698593142762 0.2259337034053303 chrMT 16571 5929 0.3577937360448977 0.6502039127651519 chrX 155270560 7044714 0.0453705712145303 0.2786819164683163 chrY 59373566 302826 0.005100350549940019 0.11518464334343953