BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238322.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 = 2,067,160 number of mapped reads = 1,854,658 (89.72%) number of supplementary alignments = 23,970 (1.16%) number of secondary alignments = 0 number of mapped bases = 123,325,411 bp number of sequenced bases = 123,268,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,142 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2092 >>>>>>> ACTG content number of A's = 34,735,019 bp (28.18%) number of C's = 22,884,067 bp (18.56%) number of T's = 38,941,280 bp (31.59%) number of G's = 26,669,095 bp (21.63%) number of N's = 38,931 bp (0.03%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,019,405 number of insertions = 9,488 mapped reads with insertion percentage = 0.51% number of deletions = 32,776 mapped reads with deletion percentage = 1.75% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.4179X There is a 3.18% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10567906 0.042398714826070584 0.8121175783361332 chr2 243199373 10852149 0.04462243823301304 0.4288460680090525 chr3 198022430 8405384 0.04244662586960477 0.24814743344410364 chr4 191154276 10138114 0.05303629200531198 0.3042694329632391 chr5 180915260 3484424 0.019259978400937544 0.17235035060783732 chr6 171115067 7806215 0.04561968233925304 0.2861808524413762 chr7 159138663 6200605 0.03896353584420902 0.44750064402268236 chr8 146364022 5026762 0.03434424615634025 0.6817880958992155 chr9 141213431 5714642 0.040468119494950876 0.39868411876616333 chr10 135534747 5441072 0.0401452182590491 0.38892666333056847 chr11 135006516 4054302 0.030030417198529884 0.27443738398415324 chr12 133851895 6738038 0.05033950397190865 0.2827625504641545 chr13 115169878 2925675 0.025403126675188455 0.18997829095771218 chr14 107349540 4528064 0.04218056267404593 0.2897082642888796 chr15 102531392 3402734 0.03318724084034673 0.2210293445023778 chr16 90354753 3985566 0.04411019750117628 0.2885969064159955 chr17 81195210 3306808 0.04072663892365079 0.26654468830718586 chr18 78077248 2377264 0.030447589546188925 0.7405133982104614 chr19 59128983 2623795 0.044374093158341656 0.5154808805197807 chr20 63025520 2981482 0.0473059484475495 0.274484660685648 chr21 48129895 2007548 0.041711040508191424 0.27666400401421554 chr22 51304566 1542063 0.03005703235068785 0.20620907778027311 chrMT 16571 10373 0.6259730855108322 0.9470723530660599 chrX 155270560 8832549 0.0568848917657024 0.31883438056219154 chrY 59373566 371877 0.00626334284856665 0.1681888815152708