BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231748.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 = 4,335,934 number of mapped reads = 4,092,751 (94.39%) number of supplementary alignments = 19,278 (0.44%) number of secondary alignments = 0 number of mapped bases = 277,829,090 bp number of sequenced bases = 277,733,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 299,349 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5126 >>>>>>> ACTG content number of A's = 73,638,299 bp (26.51%) number of C's = 52,976,034 bp (19.07%) number of T's = 80,449,755 bp (28.97%) number of G's = 70,608,957 bp (25.42%) number of N's = 60,223 bp (0.02%) GC percentage = 44.5% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,814,129 number of insertions = 18,779 mapped reads with insertion percentage = 0.45% number of deletions = 58,557 mapped reads with deletion percentage = 1.42% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0897X std coverageData = 17.0898X There is a 6.55% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 31871698 0.12787008462458355 0.9946815316609957 chr2 243199373 25381452 0.1043647920917954 60.93495570303375 chr3 198022430 24113560 0.12177186190473473 0.44401406905156254 chr4 191154276 15150416 0.0792575312309519 0.38640361449850846 chr5 180915260 16132554 0.08917188080209486 0.38124791044899176 chr6 171115067 23066931 0.13480362310818603 0.710197272547695 chr7 159138663 13872714 0.08717374985109684 0.8195628002531338 chr8 146364022 12747720 0.08709599412347387 0.6451480774205538 chr9 141213431 9277069 0.0656953728431115 0.6982873165344744 chr10 135534747 10001160 0.07379037642649675 0.4881747757160593 chr11 135006516 8794445 0.0651408929032729 0.6515757043007168 chr12 133851895 7598191 0.05676565879026218 0.3108777610529751 chr13 115169878 9447232 0.08202867072586462 0.3622487973975966 chr14 107349540 11288886 0.10516007800312885 0.5418343578794831 chr15 102531392 6285850 0.06130658988809983 0.3159271938986437 chr16 90354753 5035201 0.05572701858860706 0.39638538423643693 chr17 81195210 7592338 0.09350721551185101 0.4661386432693844 chr18 78077248 8828912 0.11307919049605847 1.4603066394557236 chr19 59128983 6544558 0.11068274250548162 0.7448971908047631 chr20 63025520 6306868 0.10006848019659338 0.42299648085927877 chr21 48129895 4759638 0.09889151015185053 0.46812080067474904 chr22 51304566 2882454 0.05618318650234757 0.29873000962970764 chrMT 16571 11683 0.7050268541427795 1.323754904019828 chrX 155270560 10254120 0.06604033630071277 0.460746090880985 chrY 59373566 583440 0.009826595222527143 0.1782777950959454