BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976564.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 686,734,540 number of mapped reads = 676,744,656 (98.55%) number of supplementary alignments = 2,102,703 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 340,063,764 number of mapped paired reads (second in pair) = 336,680,892 number of mapped paired reads (both in pair) = 671,449,108 number of mapped paired reads (singletons) = 5,295,548 number of mapped bases = 96,473,407,576 bp number of sequenced bases = 96,440,494,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,214,909 duplication rate = 13.57% >>>>>>> Insert size mean insert size = 23,125.3143 std insert size = 1,435,959.5054 median insert size = 408 >>>>>>> Mapping quality mean mapping quality = 54.4258 >>>>>>> ACTG content number of A's = 28,342,543,005 bp (29.39%) number of C's = 19,794,080,951 bp (20.52%) number of T's = 28,510,431,299 bp (29.56%) number of G's = 19,791,270,795 bp (20.52%) number of N's = 2,168,358 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 813,880,555 number of insertions = 10,366,590 mapped reads with insertion percentage = 1.44% number of deletions = 11,836,874 mapped reads with deletion percentage = 1.67% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 31.1637X std coverageData = 323.248X There is a 92.28% of reference with a coverageData >= 1X There is a 92.23% of reference with a coverageData >= 2X There is a 92.18% of reference with a coverageData >= 3X There is a 92.12% of reference with a coverageData >= 4X There is a 92.06% of reference with a coverageData >= 5X There is a 91.98% of reference with a coverageData >= 6X There is a 91.87% of reference with a coverageData >= 7X There is a 91.74% of reference with a coverageData >= 8X There is a 91.56% of reference with a coverageData >= 9X There is a 91.31% of reference with a coverageData >= 10X There is a 91% of reference with a coverageData >= 11X There is a 90.59% of reference with a coverageData >= 12X There is a 90.09% of reference with a coverageData >= 13X There is a 89.48% of reference with a coverageData >= 14X There is a 88.76% of reference with a coverageData >= 15X There is a 87.95% of reference with a coverageData >= 16X There is a 87.04% of reference with a coverageData >= 17X There is a 86.03% of reference with a coverageData >= 18X There is a 84.94% of reference with a coverageData >= 19X There is a 83.73% of reference with a coverageData >= 20X There is a 82.41% of reference with a coverageData >= 21X There is a 80.92% of reference with a coverageData >= 22X There is a 79.24% of reference with a coverageData >= 23X There is a 77.33% of reference with a coverageData >= 24X There is a 75.13% of reference with a coverageData >= 25X There is a 72.62% of reference with a coverageData >= 26X There is a 69.77% of reference with a coverageData >= 27X There is a 66.55% of reference with a coverageData >= 28X There is a 62.99% of reference with a coverageData >= 29X There is a 59.1% of reference with a coverageData >= 30X There is a 54.92% of reference with a coverageData >= 31X There is a 50.52% of reference with a coverageData >= 32X There is a 45.98% of reference with a coverageData >= 33X There is a 41.37% of reference with a coverageData >= 34X There is a 36.79% of reference with a coverageData >= 35X There is a 32.33% of reference with a coverageData >= 36X There is a 28.07% of reference with a coverageData >= 37X There is a 24.07% of reference with a coverageData >= 38X There is a 20.4% of reference with a coverageData >= 39X There is a 17.08% of reference with a coverageData >= 40X There is a 14.14% of reference with a coverageData >= 41X There is a 11.58% of reference with a coverageData >= 42X There is a 9.4% of reference with a coverageData >= 43X There is a 7.56% of reference with a coverageData >= 44X There is a 6.04% of reference with a coverageData >= 45X There is a 4.8% of reference with a coverageData >= 46X There is a 3.81% of reference with a coverageData >= 47X There is a 3.03% of reference with a coverageData >= 48X There is a 2.42% of reference with a coverageData >= 49X There is a 1.95% of reference with a coverageData >= 50X There is a 1.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7974258714 31.992934188115825 769.0888034214435 chr2 243199373 8361015709 34.37926506907565 192.47378993939046 chr3 198022430 6440441150 32.52379616793916 16.1139373356755 chr4 191154276 6454289498 33.76481883146574 222.65711563921158 chr5 180915260 5897715641 32.59932656316554 28.926517727400796 chr6 171115067 5619313093 32.83938224446361 134.9052479629711 chr7 159138663 5322025524 33.44269345784311 330.02925575575085 chr8 146364022 4923788803 33.64070442803219 228.9916225392443 chr9 141213431 4272663763 30.256780341241054 595.2598393988494 chr10 135534747 5014324640 36.99659866558057 564.0979075884619 chr11 135006516 4464223395 33.066725423830654 132.62130775091836 chr12 133851895 4303726682 32.15290065187347 18.087262821539525 chr13 115169878 3099634636 26.91358790881067 16.07150722734814 chr14 107349540 2927019895 27.26625465744893 22.25427365143181 chr15 102531392 2750966294 26.830478357301537 17.226779946052353 chr16 90354753 3029639662 33.530495755989726 189.16666479316046 chr17 81195210 2712686101 33.40943512554497 187.28941775506317 chr18 78077248 2755687564 35.29437364390712 450.1722414580206 chr19 59128983 1912248831 32.340296314584 323.879625067278 chr20 63025520 2048813005 32.50767316160184 53.16300894452148 chr21 48129895 1364183570 28.34378861620205 90.17829306305995 chr22 51304566 1186328107 23.123246125890628 64.6371816769703 chrMT 16571 106658821 6436.474624343733 771.7684242916446 chrX 155270560 2579780988 16.61474646578205 37.37942104470003 chrY 59373566 951973490 16.033624963674914 248.2852242309985