BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236128.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,368,860 number of mapped reads = 2,847,416 (84.52%) number of supplementary alignments = 17,859 (0.53%) number of secondary alignments = 0 number of mapped bases = 187,961,280 bp number of sequenced bases = 187,869,336 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,987 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9986 >>>>>>> ACTG content number of A's = 54,079,505 bp (28.79%) number of C's = 35,370,358 bp (18.83%) number of T's = 58,049,683 bp (30.9%) number of G's = 40,367,922 bp (21.49%) number of N's = 1,868 bp (0%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,414,008 number of insertions = 13,830 mapped reads with insertion percentage = 0.48% number of deletions = 53,231 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.17% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.5063X There is a 4.8% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13244615 0.053137741229539404 0.6824205011145058 chr2 243199373 17723222 0.07287527834210329 0.6077280390608719 chr3 198022430 13295294 0.06714034364692929 0.31302852068864545 chr4 191154276 10493026 0.05489297032518383 0.31006508493555107 chr5 180915260 8020821 0.04433468464738685 0.2618435480651041 chr6 171115067 16656975 0.09734370731947292 0.554872013178668 chr7 159138663 12052906 0.07573838923103181 0.5510944989218608 chr8 146364022 11768457 0.0804053949815618 1.1512924020281474 chr9 141213431 9269641 0.06564277161426664 0.5337010100474447 chr10 135534747 8196082 0.06047218282703549 0.42079225334504894 chr11 135006516 6296832 0.046640948796871404 0.34297745567637544 chr12 133851895 8035592 0.060033457128119104 0.31791689418662505 chr13 115169878 8390407 0.07285244324041049 0.32729794252955885 chr14 107349540 4890154 0.0455535626887642 0.32867400760438803 chr15 102531392 4684233 0.04568584224429529 0.2660011957291059 chr16 90354753 4039447 0.044706524735892976 0.3172221996568729 chr17 81195210 3055958 0.0376371709611934 0.2652014290040747 chr18 78077248 6009117 0.07696373980804241 0.8355602806895259 chr19 59128983 3889377 0.06577784366763081 0.4802563797851085 chr20 63025520 5031951 0.07983989660061512 0.35592118920213767 chr21 48129895 2526874 0.0525011326120699 0.32537256154377503 chr22 51304566 1609154 0.031364732721840004 0.21040182586508113 chrMT 16571 28384 1.7128718846177056 1.9542683417161262 chrX 155270560 8369927 0.05390543448803173 0.32469667335190494 chrY 59373566 382834 0.0064478862529496715 0.1802411558044076