BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068097.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,631,557 number of mapped reads = 2,205,679 (83.82%) number of supplementary alignments = 21,936 (0.83%) number of secondary alignments = 0 number of mapped bases = 141,689,943 bp number of sequenced bases = 141,632,903 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 264,516 duplication rate = 9.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2664 >>>>>>> ACTG content number of A's = 38,567,832 bp (27.23%) number of C's = 25,443,232 bp (17.96%) number of T's = 45,697,952 bp (32.27%) number of G's = 31,921,196 bp (22.54%) number of N's = 2,691 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,108,479 number of insertions = 10,938 mapped reads with insertion percentage = 0.49% number of deletions = 35,662 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0458X std coverageData = 0.4484X There is a 2.76% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 14410562 0.057815551039289086 0.5007974766138301 chr2 243199373 12454115 0.05120948646524677 0.6739916075224286 chr3 198022430 9060961 0.0457572457827126 0.329912466614496 chr4 191154276 3759935 0.019669635849527113 0.24633092537018408 chr5 180915260 4553154 0.025167329721108102 0.24639318312649913 chr6 171115067 4228462 0.024711219614576663 0.27990620675002437 chr7 159138663 11536695 0.0724946080513445 0.4828785213350135 chr8 146364022 3180818 0.0217322396346829 0.5993465907650747 chr9 141213431 2989639 0.021171066936260474 0.3586502195581906 chr10 135534747 3085662 0.022766575127778858 0.38551034198776596 chr11 135006516 9650186 0.07147940918644252 0.6743455334428397 chr12 133851895 16345863 0.12211902565891951 0.5370176860774327 chr13 115169878 8784819 0.07627705397065715 0.4298618388162376 chr14 107349540 1647192 0.015344192439017438 0.20220161825288238 chr15 102531392 1699322 0.016573675309118987 0.22347930282742473 chr16 90354753 2745762 0.03038868359254991 0.2961856639640557 chr17 81195210 2551708 0.03142682924275952 0.33141304450097825 chr18 78077248 2462890 0.03154427266698744 0.6051854653442288 chr19 59128983 1799619 0.030435480346414887 0.3282494378050798 chr20 63025520 2243103 0.03559039259017617 0.2947157986656545 chr21 48129895 3567289 0.07411794686026221 0.4498587681933646 chr22 51304566 734469 0.014315860307638116 0.17540831658751604 chrMT 16571 61486 3.710458029086959 3.4845938580049705 chrX 155270560 17241605 0.11104233152762506 0.5383461074041438 chrY 59373566 894627 0.015067766015603645 0.526241854024826