BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008694.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 = 2,281,743 number of mapped reads = 1,928,613 (84.52%) number of supplementary alignments = 7,330 (0.32%) number of secondary alignments = 0 number of mapped bases = 121,762,953 bp number of sequenced bases = 121,680,775 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,010 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.66 >>>>>>> ACTG content number of A's = 32,002,867 bp (26.3%) number of C's = 22,699,121 bp (18.65%) number of T's = 37,698,124 bp (30.98%) number of G's = 29,251,418 bp (24.04%) number of N's = 29,245 bp (0.02%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,222,621 number of insertions = 10,797 mapped reads with insertion percentage = 0.56% number of deletions = 50,640 mapped reads with deletion percentage = 2.59% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.3547X There is a 3.22% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% 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% 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 9345592 0.037494759140439614 0.43304560581946644 chr2 243199373 10710799 0.04404122785300108 0.49301568089374187 chr3 198022430 9430277 0.04762226683108575 0.26752245954577886 chr4 191154276 6216610 0.03252142787535655 0.23761130501795827 chr5 180915260 6302315 0.034835729169557066 0.2248446016925899 chr6 171115067 6335659 0.03702572257999934 0.26829388633004025 chr7 159138663 7032802 0.04419291872522518 0.5956835703072649 chr8 146364022 9543160 0.06520154249382407 0.37956961284792895 chr9 141213431 4252184 0.030111753321821068 0.36231955360301404 chr10 135534747 6529577 0.048176406010482314 0.3727421865019715 chr11 135006516 5623275 0.0416518784915537 0.4777094015018545 chr12 133851895 5535365 0.041354401444970205 0.25200706745520474 chr13 115169878 3490602 0.030308289464368452 0.2136961569969945 chr14 107349540 4298151 0.040038839477095106 0.25584897489760666 chr15 102531392 3493042 0.03406802474699651 0.22966350588456377 chr16 90354753 3500477 0.03874148159090203 0.2638720238146442 chr17 81195210 3346489 0.04121535001880037 0.30833859031819044 chr18 78077248 2282969 0.029239875360361062 0.5230110563239949 chr19 59128983 2563275 0.04335056802854194 0.35689394955914344 chr20 63025520 2861524 0.04540262420682924 0.26649995011794775 chr21 48129895 1356348 0.028180988136375533 0.22205452398366832 chr22 51304566 1596341 0.031114988868632083 0.20968947099350657 chrMT 16571 104416 6.301128477460624 5.483600569621915 chrX 155270560 5658658 0.036443856452891006 0.2612875317921409 chrY 59373566 353046 0.005946181504408881 0.14309367664244552