BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717046.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 = 1,596,873 number of mapped reads = 1,491,136 (93.38%) number of supplementary alignments = 44,090 (2.76%) number of secondary alignments = 0 number of mapped bases = 111,122,438 bp number of sequenced bases = 111,085,078 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,152 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7774 >>>>>>> ACTG content number of A's = 27,937,657 bp (25.15%) number of C's = 23,218,632 bp (20.9%) number of T's = 32,856,771 bp (29.58%) number of G's = 27,058,989 bp (24.36%) number of N's = 13,029 bp (0.01%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 843,672 number of insertions = 9,486 mapped reads with insertion percentage = 0.63% number of deletions = 21,618 mapped reads with deletion percentage = 1.43% homopolymer indels = 40.02% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.2892X There is a 3.19% of reference with a coverageData >= 1X There is a 0.29% 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 10245003 0.04110321955827745 0.32518723847766556 chr2 243199373 9855603 0.040524787866126614 0.4976960602173478 chr3 198022430 7674252 0.038754458270207064 0.21539835764768744 chr4 191154276 4337657 0.02269191718211943 0.17249167267339072 chr5 180915260 5706057 0.031539943065057086 0.1923892984357378 chr6 171115067 7498574 0.043821821955631765 0.2446751773602942 chr7 159138663 5454373 0.034274342244536765 0.3522788043954793 chr8 146364022 7120118 0.0486466407707763 0.39174507150842586 chr9 141213431 5725452 0.04054467028706356 0.2940165259788001 chr10 135534747 6368536 0.046988216239485806 0.3154518548674399 chr11 135006516 5143949 0.0381014868941585 0.27039258549883116 chr12 133851895 5834174 0.04358678672423726 0.2341266241788825 chr13 115169878 3333370 0.028943071381911163 0.18531923558944954 chr14 107349540 2656962 0.024750567165914266 0.18349831000866423 chr15 102531392 2299451 0.022426799784401638 0.16133757623641398 chr16 90354753 2962375 0.03278604502410626 0.21503124652831535 chr17 81195210 3445478 0.042434498291216934 0.2505315773545265 chr18 78077248 3030007 0.03880780992690726 0.4132362487197251 chr19 59128983 2031172 0.03435154634741477 0.31220296245133716 chr20 63025520 2054617 0.032599762762766576 0.20123448883660278 chr21 48129895 1845973 0.03835397937186441 0.22499338880630493 chr22 51304566 1545664 0.030127221035258344 0.19354937978586345 chrMT 16571 101522 6.126486029811116 5.601926581612412 chrX 155270560 4579634 0.029494541656834367 0.21892026173384765 chrY 59373566 272465 0.004588995042002362 0.1343141800142325