BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524297.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 = 2,113,956 number of mapped reads = 1,926,623 (91.14%) number of supplementary alignments = 8,194 (0.39%) number of secondary alignments = 0 number of mapped bases = 111,882,057 bp number of sequenced bases = 111,852,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,513 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7248 >>>>>>> ACTG content number of A's = 26,491,451 bp (23.68%) number of C's = 22,912,373 bp (20.48%) number of T's = 35,886,841 bp (32.08%) number of G's = 26,545,578 bp (23.73%) number of N's = 15,792 bp (0.01%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 576,342 number of insertions = 6,497 mapped reads with insertion percentage = 0.34% number of deletions = 19,219 mapped reads with deletion percentage = 0.99% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.3438X There is a 3.23% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% 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 9556858 0.038342363849115546 0.6809617065900236 chr2 243199373 7212685 0.029657498335737897 0.43959118867049424 chr3 198022430 7941710 0.04010510324512228 0.22185148929021084 chr4 191154276 5871278 0.03071486614298913 0.21070491134747887 chr5 180915260 6660889 0.03681772891905304 0.21088978195237448 chr6 171115067 7056096 0.041235971347865004 0.2461229304275126 chr7 159138663 5234632 0.03289352757726763 0.44540882842260876 chr8 146364022 11079258 0.07569659434474955 0.40364129375515995 chr9 141213431 4634105 0.03281631900863594 0.26407107143449826 chr10 135534747 6092282 0.04494996401181167 0.34394634236403776 chr11 135006516 5356418 0.03967525537804412 0.285415054300858 chr12 133851895 4468913 0.03338699836860733 0.20325538978749583 chr13 115169878 2855572 0.024794434530876208 0.17162895689051552 chr14 107349540 2414639 0.022493240306386036 0.18267245075082988 chr15 102531392 3392428 0.03308672528312109 0.20497280343365207 chr16 90354753 3437070 0.03803972548073924 0.22873243178560632 chr17 81195210 3291654 0.04054000229816512 0.24606502544969797 chr18 78077248 2633642 0.03373123499434816 0.48578784911382417 chr19 59128983 1983609 0.033547152333061436 0.4715973590853532 chr20 63025520 2473693 0.03924906926591006 0.218732350763209 chr21 48129895 1616445 0.033585051452948315 0.21691287183313598 chr22 51304566 785790 0.015316180630004745 0.13508201212360627 chrMT 16571 3931 0.2372216522841108 0.4980489170015929 chrX 155270560 5521343 0.03555949691944178 0.23670230563308498 chrY 59373566 307117 0.005172621769088284 0.13684512764097007