BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013212.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 = 826,746 number of mapped reads = 653,792 (79.08%) number of supplementary alignments = 4,582 (0.55%) number of secondary alignments = 0 number of mapped bases = 43,592,315 bp number of sequenced bases = 43,570,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,077 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5275 >>>>>>> ACTG content number of A's = 13,275,215 bp (30.47%) number of C's = 7,527,678 bp (17.28%) number of T's = 13,419,741 bp (30.8%) number of G's = 9,347,431 bp (21.45%) number of N's = 531 bp (0%) GC percentage = 38.73% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 371,003 number of insertions = 2,881 mapped reads with insertion percentage = 0.44% number of deletions = 12,643 mapped reads with deletion percentage = 1.92% homopolymer indels = 50.05% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 0.1361X There is a 1.32% of reference with a coverageData >= 1X There is a 0.07% 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 3497484 0.014031997135926896 0.1724716272957727 chr2 243199373 5527754 0.022729310243739816 0.16677879809049653 chr3 198022430 2712782 0.013699367288847027 0.12229436489785246 chr4 191154276 2842291 0.014869094531790646 0.12822354182442589 chr5 180915260 2044246 0.011299466943805625 0.11111489653511425 chr6 171115067 1809646 0.010575608751040024 0.11102858051057587 chr7 159138663 2675554 0.01681272136865948 0.17162966618751224 chr8 146364022 2699234 0.018441922838113863 0.1655294538408401 chr9 141213431 1420378 0.010058377520761464 0.11243639588094671 chr10 135534747 1899058 0.01401159512254079 0.13564421538772609 chr11 135006516 1815882 0.013450328575251878 0.13004050548612286 chr12 133851895 2733358 0.02042076430819302 0.14955293755534504 chr13 115169878 855955 0.007432108246220422 0.08931993007414 chr14 107349540 1493791 0.013915206343688105 0.12422974924443009 chr15 102531392 1227651 0.011973415907588575 0.11540476367708281 chr16 90354753 1338173 0.014810211478304854 0.12809740094437513 chr17 81195210 862475 0.010622239907994572 0.11182736121630026 chr18 78077248 998387 0.012787169445316516 0.15676433853856647 chr19 59128983 660308 0.01116724770997668 0.12914819809180236 chr20 63025520 856142 0.013584052936017029 0.12196661516822585 chr21 48129895 873016 0.018138747238073134 0.1433846471246569 chr22 51304566 303662 0.005918810423228217 0.07997915987723266 chrMT 16571 5128 0.30945627904169937 0.6300037501372698 chrX 155270560 2370728 0.01526836768026083 0.131703092999512 chrY 59373566 69232 0.0011660407933052226 0.03706593789037255