BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524438.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 = 2,947,749 number of mapped reads = 2,709,527 (91.92%) number of supplementary alignments = 12,448 (0.42%) number of secondary alignments = 0 number of mapped bases = 157,551,042 bp number of sequenced bases = 157,507,440 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,265 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4414 >>>>>>> ACTG content number of A's = 36,183,093 bp (22.97%) number of C's = 33,111,807 bp (21.02%) number of T's = 49,814,630 bp (31.63%) number of G's = 38,382,915 bp (24.37%) number of N's = 14,995 bp (0.01%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 797,620 number of insertions = 11,690 mapped reads with insertion percentage = 0.43% number of deletions = 26,536 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.04% >>>>>>> Coverage mean coverageData = 0.0509X std coverageData = 0.4839X There is a 4.17% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 13255250 0.05318040912724546 1.0236695941432605 chr2 243199373 12908414 0.05307749703779047 0.6643389384422114 chr3 198022430 10555546 0.053304799865348584 0.27686522799423546 chr4 191154276 10060166 0.05262851666472792 0.3749179703039625 chr5 180915260 9468454 0.05233640324204824 0.270083763930288 chr6 171115067 6137916 0.035870108387357845 0.2513406444541576 chr7 159138663 9010906 0.05662298419586446 0.6474584473482088 chr8 146364022 8195944 0.05599698537937144 0.3525622755444793 chr9 141213431 5761626 0.04080083572220549 0.30925149153727666 chr10 135534747 8077748 0.059599093065042574 0.5369021932822569 chr11 135006516 6507691 0.04820279193042801 0.33839284446423384 chr12 133851895 7331154 0.05477064034095296 0.2856917847669687 chr13 115169878 4933197 0.04283409069861131 0.24502517748284938 chr14 107349540 4399826 0.04098597907359454 0.2520443949881434 chr15 102531392 4889264 0.04768553225142989 0.26145469842059477 chr16 90354753 5114590 0.05660565526641415 0.3134676410857589 chr17 81195210 4647117 0.057233881161216284 0.31795411385777306 chr18 78077248 4206705 0.0538787560750092 0.5658429132008197 chr19 59128983 4882774 0.08257835248071153 0.662121013073174 chr20 63025520 4484982 0.07116136447585042 0.3416438209597468 chr21 48129895 2154260 0.044759291496480516 0.33939223693234305 chr22 51304566 1230668 0.023987494602332276 0.1868534183872293 chrMT 16571 33655 2.0309576971818237 2.2137089189985564 chrX 155270560 8709999 0.0560956243089482 0.3132919336407694 chrY 59373566 593190 0.009990809714882209 0.3476580036893008