BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524679.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 = 1,307,326 number of mapped reads = 1,213,002 (92.78%) number of supplementary alignments = 5,205 (0.4%) number of secondary alignments = 0 number of mapped bases = 72,183,057 bp number of sequenced bases = 72,161,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,557 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0098 >>>>>>> ACTG content number of A's = 18,439,985 bp (25.55%) number of C's = 14,170,417 bp (19.64%) number of T's = 22,459,512 bp (31.12%) number of G's = 17,081,922 bp (23.67%) number of N's = 9,581 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 357,282 number of insertions = 5,029 mapped reads with insertion percentage = 0.41% number of deletions = 13,648 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2343X There is a 2.14% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5771358 0.023154839000381067 0.41559972040161697 chr2 243199373 6154086 0.02530469517287777 0.289376408270465 chr3 198022430 4780460 0.024141002612683825 0.16534260207743517 chr4 191154276 4707705 0.024627777617697653 0.18660934800819015 chr5 180915260 4306289 0.02380279585038874 0.16459927785898024 chr6 171115067 4140529 0.024197337339090075 0.1815702657183716 chr7 159138663 3967970 0.02493404132721663 0.2699355396220023 chr8 146364022 3667111 0.025054729638407998 0.2596716192499219 chr9 141213431 3053973 0.02162664683078198 0.19566040117805605 chr10 135534747 3525027 0.02600828996272078 0.24783843304076686 chr11 135006516 3311143 0.024525801406503966 0.20128011623010683 chr12 133851895 3224097 0.02408704785240433 0.16795646900303715 chr13 115169878 2287128 0.019858734242993642 0.15027319337569306 chr14 107349540 2162435 0.02014386833888622 0.15648856827896668 chr15 102531392 2082272 0.02030862899042666 0.15229587954254495 chr16 90354753 2112181 0.023376534491771562 0.1736932192484382 chr17 81195210 1933826 0.023816996101124685 0.1732306457695824 chr18 78077248 1934344 0.024774746159085936 0.35274977021345455 chr19 59128983 1472071 0.024895929632342908 0.3230447328526977 chr20 63025520 1509485 0.023950377561343404 0.16797168669109672 chr21 48129895 961446 0.01997606684992768 0.17117837952445744 chr22 51304566 826762 0.016114784013571033 0.13560244972975513 chrMT 16571 16972 1.0241989016957336 1.2033721008471974 chrX 155270560 4035579 0.025990625653697648 0.1856138378811437 chrY 59373566 238808 0.004022126614392675 0.1496189183432434