BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714256.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 279,386 number of mapped reads = 164,466 (58.87%) number of supplementary alignments = 1,487 (0.53%) number of secondary alignments = 0 number of mapped bases = 19,300,273 bp number of sequenced bases = 19,234,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,038 duplication rate = 30.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 19.164 >>>>>>> ACTG content number of A's = 5,981,068 bp (31.09%) number of C's = 3,397,286 bp (17.66%) number of T's = 5,232,381 bp (27.2%) number of G's = 4,624,132 bp (24.04%) number of N's = 120 bp (0%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0386 number of mismatches = 607,023 number of insertions = 58,407 mapped reads with insertion percentage = 34.82% number of deletions = 24,892 mapped reads with deletion percentage = 14.36% homopolymer indels = 64.65% >>>>>>> Coverage mean coverageData = 0.0062X std coverageData = 24.11X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 52595 2.1101251338507198E-4 0.05934587982723987 chr2 243199373 1082185 0.004449785320786991 4.414311903424951 chr3 198022430 576724 0.0029124175478505137 3.009825391410709 chr4 191154276 45476 2.379020807256229E-4 0.04855555545218216 chr5 180915260 29522 1.631813701066455E-4 0.034678011338179444 chr6 171115067 44690 2.611692867466779E-4 0.05582836715009222 chr7 159138663 884744 0.005559579195408975 5.355401423946518 chr8 146364022 32685 2.233130762148638E-4 0.04636848520591663 chr9 141213431 22171 1.5700347936450888E-4 0.02909618870372749 chr10 135534747 15835767 0.11683916744980533 114.86144254767663 chr11 135006516 21661 1.6044410774958447E-4 0.03959371399889195 chr12 133851895 24554 1.834415568042574E-4 0.04868414537865512 chr13 115169878 25974 2.2552772001720796E-4 0.06097980288782023 chr14 107349540 226013 0.0021053932788160992 1.426222874794103 chr15 102531392 17432 1.7001622293394788E-4 0.06190699484623197 chr16 90354753 18580 2.0563389731141206E-4 0.08324401183544294 chr17 81195210 86285 0.0010626858407041498 0.6459961320688719 chr18 78077248 7736 9.908136106436539E-5 0.019148512530887576 chr19 59128983 5905 9.986642252920197E-5 0.018140677030339496 chr20 63025520 6186 9.815071736020584E-5 0.02314129864780958 chr21 48129895 64454 0.001339167683619505 0.1991790043475617 chr22 51304566 6259 1.2199693882996691E-4 0.029230997539692313 chrMT 16571 41639 2.512763261118822 20.485689331352074 chrX 155270560 136778 8.809010542629588E-4 0.11677916697964578 chrY 59373566 4258 7.171541625106365E-5 0.02077298494880038