BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716481.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,717,586 number of mapped reads = 1,585,279 (92.3%) number of supplementary alignments = 9,208 (0.54%) number of secondary alignments = 0 number of mapped bases = 92,581,974 bp number of sequenced bases = 92,555,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,319 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9097 >>>>>>> ACTG content number of A's = 22,867,662 bp (24.71%) number of C's = 17,680,140 bp (19.1%) number of T's = 29,410,156 bp (31.78%) number of G's = 22,597,167 bp (24.41%) number of N's = 623 bp (0%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 455,889 number of insertions = 6,166 mapped reads with insertion percentage = 0.39% number of deletions = 16,548 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2629X There is a 2.63% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10872235 0.0436196907208508 0.4074392731540541 chr2 243199373 9324520 0.03834105279539516 0.3776743719524084 chr3 198022430 5857672 0.029580851017735717 0.1903302441138406 chr4 191154276 3908922 0.020449042949999195 0.18199617098727452 chr5 180915260 6624598 0.0366171322419126 0.21276246705358887 chr6 171115067 3453840 0.020184312583064353 0.17479211603689737 chr7 159138663 6247001 0.039255080332049795 0.39462056708283266 chr8 146364022 4104103 0.028040381399193855 0.24365390160664221 chr9 141213431 2536781 0.017964162346568863 0.2007277802507055 chr10 135534747 4249986 0.03135716924310192 0.24292390045074225 chr11 135006516 3959858 0.029330865778359912 0.25221599616840973 chr12 133851895 3674590 0.0274526557879513 0.1858639352964905 chr13 115169878 2687070 0.023331361000486602 0.16848546105575146 chr14 107349540 1997533 0.018607746246513956 0.15885430749594606 chr15 102531392 3972545 0.038744670510276503 0.22013386446643773 chr16 90354753 2821334 0.031225075674768323 0.20720732206360587 chr17 81195210 3502537 0.04313723679019982 0.2478927737180414 chr18 78077248 2942200 0.037683192932209904 0.40966562056118344 chr19 59128983 1471630 0.0248884713609906 0.3010762097679056 chr20 63025520 2471040 0.03920697520623392 0.22403763703262142 chr21 48129895 1189132 0.024706723336919808 0.1846815664391002 chr22 51304566 1075604 0.020965073557000755 0.1600085304867619 chrMT 16571 1640 0.09896807676060587 0.3473819385333013 chrX 155270560 3412880 0.021980213119602326 0.18462980723344496 chrY 59373566 222723 0.0037512148082869067 0.10022264876306101