BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716668.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 = 1,442,257 number of mapped reads = 1,325,135 (91.88%) number of supplementary alignments = 27,450 (1.9%) number of secondary alignments = 0 number of mapped bases = 104,335,762 bp number of sequenced bases = 104,286,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,057 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2338 >>>>>>> ACTG content number of A's = 27,374,057 bp (26.25%) number of C's = 20,147,982 bp (19.32%) number of T's = 32,359,738 bp (31.03%) number of G's = 24,397,204 bp (23.39%) number of N's = 7,257 bp (0.01%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 699,146 number of insertions = 9,242 mapped reads with insertion percentage = 0.69% number of deletions = 25,785 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 0.3311X There is a 2.99% 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 0.01% 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 10479132 0.04204255121996266 0.7151674755786545 chr2 243199373 8750295 0.0359799241752157 0.33225070776732923 chr3 198022430 6699104 0.03383002622480696 0.2004676894088626 chr4 191154276 6457751 0.03378292725191248 0.23773577655295677 chr5 180915260 6060979 0.033501756568240844 0.19892968775660125 chr6 171115067 5733685 0.03350777404072781 0.21263722575917135 chr7 159138663 5593640 0.03514947213047781 0.3755067505156813 chr8 146364022 2805658 0.01916904141920888 0.3268380800521958 chr9 141213431 4280880 0.03031496345414906 0.27471484390186707 chr10 135534747 4913201 0.036250490068056127 0.31022619202601665 chr11 135006516 6152080 0.045568763510644185 0.3469765966534895 chr12 133851895 4623629 0.034542872926827076 0.20241798747718023 chr13 115169878 3635649 0.03156770731319174 0.1937270244304879 chr14 107349540 3141252 0.029261904615520477 0.1984847495447682 chr15 102531392 3070902 0.029950846663624738 0.18741762332877224 chr16 90354753 2449064 0.0271049825126521 0.19109312068214118 chr17 81195210 3815577 0.0469926366345995 0.2819864576774201 chr18 78077248 2641898 0.0338369764262183 0.42512701447698487 chr19 59128983 2241562 0.03790969988440356 0.5019562656648417 chr20 63025520 2229226 0.03537021193954449 0.2114767114500746 chr21 48129895 1321994 0.027467211387018402 0.20047486101303333 chr22 51304566 1392061 0.027133276987471252 0.17842339178515523 chrMT 16571 64704 3.9046527065355137 2.8319480246179207 chrX 155270560 5484211 0.03532035306628636 0.2327196878521597 chrY 59373566 297628 0.005012803172374723 0.16829779498639405