BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238672.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 = 4,715,776 number of mapped reads = 4,063,491 (86.17%) number of supplementary alignments = 32,422 (0.69%) number of secondary alignments = 0 number of mapped bases = 249,979,630 bp number of sequenced bases = 249,861,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,534,265 duplication rate = 21.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0643 >>>>>>> ACTG content number of A's = 61,261,201 bp (24.52%) number of C's = 45,356,909 bp (18.15%) number of T's = 82,217,467 bp (32.91%) number of G's = 61,013,408 bp (24.42%) number of N's = 12,466 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,523,711 number of insertions = 17,970 mapped reads with insertion percentage = 0.44% number of deletions = 68,817 mapped reads with deletion percentage = 1.68% homopolymer indels = 40.69% >>>>>>> Coverage mean coverageData = 0.0808X std coverageData = 1.3362X There is a 2.49% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 26898972 0.10791937806245225 1.7224481463109902 chr2 243199373 26446794 0.10874532147745299 3.07734943325881 chr3 198022430 21477623 0.10846055671572155 0.9008943690642554 chr4 191154276 8323425 0.04354297049572671 0.5426222277501651 chr5 180915260 19049726 0.10529640230459276 0.8623218712490561 chr6 171115067 10781416 0.06300681868067176 1.158186077069401 chr7 159138663 11337374 0.07124210915357508 0.9133720784935462 chr8 146364022 11914656 0.08140426750502934 1.004537211096515 chr9 141213431 12581074 0.08909261612657793 0.9463121308665492 chr10 135534747 10148475 0.07487729327446932 0.7881913741929998 chr11 135006516 17689968 0.13103047559571124 1.135860832082935 chr12 133851895 6244549 0.04665267533194058 0.5740697190589108 chr13 115169878 6454283 0.05604141562084489 0.8359926848382457 chr14 107349540 2881473 0.026841968768566683 0.4259367493118002 chr15 102531392 7008262 0.06835235397954999 0.909532473664397 chr16 90354753 6186544 0.06846949158280584 0.9345045202851588 chr17 81195210 7429724 0.09150446190113924 0.8513521718510139 chr18 78077248 11192329 0.1433494300413867 2.7396313546241724 chr19 59128983 5109002 0.0864043611235458 1.3097279107794844 chr20 63025520 4134205 0.06559573011059647 0.7128110074884462 chr21 48129895 3270811 0.06795799159752998 0.7396512023663666 chr22 51304566 4834981 0.09424075432194476 0.8790294303657491 chrMT 16571 75712 4.5689457485969465 5.424385792806987 chrX 155270560 7651558 0.04927887166762328 0.6372454032805828 chrY 59373566 856694 0.014428879006526238 0.5743069849551866