BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264620.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,609,813,856 number of mapped reads = 1,600,471,362 (99.42%) number of supplementary alignments = 10,804,132 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 802,922,916 number of mapped paired reads (second in pair) = 797,548,446 number of mapped paired reads (both in pair) = 1,593,738,238 number of mapped paired reads (singletons) = 6,733,124 number of mapped bases = 160,657,197,023 bp number of sequenced bases = 160,620,450,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 709,325,815 duplication rate = 44.25% >>>>>>> Insert size mean insert size = 88,591.4072 std insert size = 2,850,953.9756 median insert size = 311 >>>>>>> Mapping quality mean mapping quality = 54.4737 >>>>>>> ACTG content number of A's = 49,707,757,996 bp (30.95%) number of C's = 30,620,923,718 bp (19.06%) number of T's = 49,373,361,688 bp (30.74%) number of G's = 30,891,488,076 bp (19.23%) number of N's = 26,919,035 bp (0.02%) GC percentage = 38.3% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 725,149,218 number of insertions = 17,613,950 mapped reads with insertion percentage = 1.09% number of deletions = 16,493,267 mapped reads with deletion percentage = 1.01% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 51.897X std coverageData = 52.3136X There is a 90.72% of reference with a coverageData >= 1X There is a 89.56% of reference with a coverageData >= 2X There is a 88.42% of reference with a coverageData >= 3X There is a 87.29% of reference with a coverageData >= 4X There is a 86.15% of reference with a coverageData >= 5X There is a 85.01% of reference with a coverageData >= 6X There is a 83.87% of reference with a coverageData >= 7X There is a 82.73% of reference with a coverageData >= 8X There is a 81.59% of reference with a coverageData >= 9X There is a 80.45% of reference with a coverageData >= 10X There is a 79.32% of reference with a coverageData >= 11X There is a 78.18% of reference with a coverageData >= 12X There is a 77.06% of reference with a coverageData >= 13X There is a 75.93% of reference with a coverageData >= 14X There is a 74.82% of reference with a coverageData >= 15X There is a 73.7% of reference with a coverageData >= 16X There is a 72.6% of reference with a coverageData >= 17X There is a 71.5% of reference with a coverageData >= 18X There is a 70.4% of reference with a coverageData >= 19X There is a 69.31% of reference with a coverageData >= 20X There is a 68.23% of reference with a coverageData >= 21X There is a 67.15% of reference with a coverageData >= 22X There is a 66.09% of reference with a coverageData >= 23X There is a 65.02% of reference with a coverageData >= 24X There is a 63.97% of reference with a coverageData >= 25X There is a 62.92% of reference with a coverageData >= 26X There is a 61.89% of reference with a coverageData >= 27X There is a 60.85% of reference with a coverageData >= 28X There is a 59.83% of reference with a coverageData >= 29X There is a 58.82% of reference with a coverageData >= 30X There is a 57.82% of reference with a coverageData >= 31X There is a 56.82% of reference with a coverageData >= 32X There is a 55.84% of reference with a coverageData >= 33X There is a 54.87% of reference with a coverageData >= 34X There is a 53.9% of reference with a coverageData >= 35X There is a 52.95% of reference with a coverageData >= 36X There is a 52.01% of reference with a coverageData >= 37X There is a 51.08% of reference with a coverageData >= 38X There is a 50.16% of reference with a coverageData >= 39X There is a 49.25% of reference with a coverageData >= 40X There is a 48.35% of reference with a coverageData >= 41X There is a 47.47% of reference with a coverageData >= 42X There is a 46.59% of reference with a coverageData >= 43X There is a 45.73% of reference with a coverageData >= 44X There is a 44.88% of reference with a coverageData >= 45X There is a 44.04% of reference with a coverageData >= 46X There is a 43.21% of reference with a coverageData >= 47X There is a 42.39% of reference with a coverageData >= 48X There is a 41.59% of reference with a coverageData >= 49X There is a 40.8% of reference with a coverageData >= 50X There is a 40.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12324539417 49.446373965102374 53.05476232491098 chr2 243199373 14581101418 59.95534132400909 53.50928373393443 chr3 198022430 12874200055 65.01384744647362 53.46611238577531 chr4 191154276 12977002463 67.88758658477512 53.85250874354938 chr5 180915260 11818619287 65.3268236576616 53.468202948210234 chr6 171115067 11056731118 64.61576593953588 55.39451442995677 chr7 159138663 8949947589 56.23993202079372 54.058228463327325 chr8 146364022 8685466446 59.34153986284963 50.70179318790461 chr9 141213431 6753161300 47.82237250506292 55.446156015463046 chr10 135534747 6726513511 49.62943938649179 45.99351614550417 chr11 135006516 7579912078 56.14478695235717 52.800792878044675 chr12 133851895 7759166784 57.96829984364435 57.19454342274636 chr13 115169878 6538219808 56.77022431160342 53.49769827349445 chr14 107349540 5097772926 47.48760847973825 51.65211546658718 chr15 102531392 4295070772 41.890300016603696 50.71626002015538 chr16 90354753 2893707964 32.026073537050124 38.762719222451345 chr17 81195210 2746928419 33.831163427005116 42.59125063382231 chr18 78077248 4647753974 59.52763568203633 50.06157594496368 chr19 59128983 1126516561 19.051850781874602 27.06463511381088 chr20 63025520 2376407244 37.70547619440506 48.87102507005111 chr21 48129895 2119196146 44.03076603429116 56.84691660560964 chr22 51304566 887747485 17.303479089950784 29.036176648795003 chrMT 16571 65946 3.9796029207651924 12.161678044625143 chrX 155270560 5081125546 32.72433322839822 34.22787045596701 chrY 59373566 760322766 12.805745337916877 28.913239812712554