BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716994.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 = 2,415,394 number of mapped reads = 2,244,910 (92.94%) number of supplementary alignments = 14,348 (0.59%) number of secondary alignments = 0 number of mapped bases = 132,121,896 bp number of sequenced bases = 132,084,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,619 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6506 >>>>>>> ACTG content number of A's = 34,215,351 bp (25.9%) number of C's = 27,984,132 bp (21.19%) number of T's = 39,073,731 bp (29.58%) number of G's = 30,809,417 bp (23.33%) number of N's = 1,732 bp (0%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 639,923 number of insertions = 7,418 mapped reads with insertion percentage = 0.33% number of deletions = 23,707 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.97% >>>>>>> Coverage mean coverageData = 0.0427X std coverageData = 0.3489X There is a 3.67% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12129924 0.048665571830210204 0.5678228601698143 chr2 243199373 12046061 0.0495316285210982 0.43467067839863843 chr3 198022430 8714461 0.04400744400520688 0.2400049873377243 chr4 191154276 7311143 0.03824734216251589 0.25190850094869516 chr5 180915260 7118285 0.03934596230301413 0.22500982739511094 chr6 171115067 7256587 0.04240764490949239 0.25072347508582893 chr7 159138663 6398768 0.040208758069055786 0.5773249024592482 chr8 146364022 10917561 0.07459183514374865 0.45136367211619466 chr9 141213431 5631109 0.03987658227778631 0.27097924780118626 chr10 135534747 6270905 0.04626787697475098 0.3886959114483696 chr11 135006516 4478615 0.03317332476011751 0.2671702813730854 chr12 133851895 6087940 0.045482658276896265 0.2513917832242211 chr13 115169878 3404235 0.029558379839561867 0.19445448625084708 chr14 107349540 4330148 0.040336903166981436 0.23456429029779852 chr15 102531392 3158324 0.030803483093255965 0.20070289776462014 chr16 90354753 4055471 0.04488387013796607 0.25167877673991285 chr17 81195210 5698557 0.07018341352895079 0.3209220652749276 chr18 78077248 3058756 0.03917602218766727 0.4359209011728126 chr19 59128983 2903574 0.04910576594899324 0.483689542961101 chr20 63025520 2754151 0.04369898098421084 0.2445381705497408 chr21 48129895 1397028 0.02902620086746501 0.20983550450874125 chr22 51304566 2052430 0.040004821403225595 0.22746029939882859 chrMT 16571 17297 1.0438114778830487 1.2319367861736226 chrX 155270560 4634178 0.029845825248521033 0.22922508721154503 chrY 59373566 296388 0.004991918457449566 0.13172717231856776