BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976567.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 = 1,505,194,148 number of mapped reads = 1,482,610,631 (98.5%) number of supplementary alignments = 1,783,297 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 744,298,048 number of mapped paired reads (second in pair) = 738,312,583 number of mapped paired reads (both in pair) = 1,468,159,300 number of mapped paired reads (singletons) = 14,451,331 number of mapped bases = 144,197,513,554 bp number of sequenced bases = 144,161,138,389 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 444,621,459 duplication rate = 26.98% >>>>>>> Insert size mean insert size = 17,169.9789 std insert size = 1,222,503.6597 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 53.8568 >>>>>>> ACTG content number of A's = 43,159,319,215 bp (29.94%) number of C's = 28,810,377,350 bp (19.98%) number of T's = 43,440,547,671 bp (30.13%) number of G's = 28,693,310,463 bp (19.9%) number of N's = 57,583,690 bp (0.04%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 764,978,368 number of insertions = 12,380,530 mapped reads with insertion percentage = 0.81% number of deletions = 14,703,293 mapped reads with deletion percentage = 0.96% homopolymer indels = 41.13% >>>>>>> Coverage mean coverageData = 46.58X std coverageData = 496.1623X There is a 92.38% of reference with a coverageData >= 1X There is a 92.36% of reference with a coverageData >= 2X There is a 92.35% of reference with a coverageData >= 3X There is a 92.33% of reference with a coverageData >= 4X There is a 92.31% of reference with a coverageData >= 5X There is a 92.29% of reference with a coverageData >= 6X There is a 92.26% of reference with a coverageData >= 7X There is a 92.23% of reference with a coverageData >= 8X There is a 92.2% of reference with a coverageData >= 9X There is a 92.16% of reference with a coverageData >= 10X There is a 92.11% of reference with a coverageData >= 11X There is a 92.05% of reference with a coverageData >= 12X There is a 91.97% of reference with a coverageData >= 13X There is a 91.86% of reference with a coverageData >= 14X There is a 91.73% of reference with a coverageData >= 15X There is a 91.57% of reference with a coverageData >= 16X There is a 91.37% of reference with a coverageData >= 17X There is a 91.12% of reference with a coverageData >= 18X There is a 90.83% of reference with a coverageData >= 19X There is a 90.49% of reference with a coverageData >= 20X There is a 90.1% of reference with a coverageData >= 21X There is a 89.66% of reference with a coverageData >= 22X There is a 89.17% of reference with a coverageData >= 23X There is a 88.65% of reference with a coverageData >= 24X There is a 88.08% of reference with a coverageData >= 25X There is a 87.47% of reference with a coverageData >= 26X There is a 86.83% of reference with a coverageData >= 27X There is a 86.15% of reference with a coverageData >= 28X There is a 85.42% of reference with a coverageData >= 29X There is a 84.64% of reference with a coverageData >= 30X There is a 83.79% of reference with a coverageData >= 31X There is a 82.88% of reference with a coverageData >= 32X There is a 81.87% of reference with a coverageData >= 33X There is a 80.76% of reference with a coverageData >= 34X There is a 79.53% of reference with a coverageData >= 35X There is a 78.16% of reference with a coverageData >= 36X There is a 76.64% of reference with a coverageData >= 37X There is a 74.96% of reference with a coverageData >= 38X There is a 73.11% of reference with a coverageData >= 39X There is a 71.07% of reference with a coverageData >= 40X There is a 68.86% of reference with a coverageData >= 41X There is a 66.47% of reference with a coverageData >= 42X There is a 63.91% of reference with a coverageData >= 43X There is a 61.19% of reference with a coverageData >= 44X There is a 58.33% of reference with a coverageData >= 45X There is a 55.33% of reference with a coverageData >= 46X There is a 52.23% of reference with a coverageData >= 47X There is a 49.05% of reference with a coverageData >= 48X There is a 45.82% of reference with a coverageData >= 49X There is a 42.56% of reference with a coverageData >= 50X There is a 39.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11882470442 47.67278169389195 1226.782422791964 chr2 243199373 12561003908 51.648997910862214 299.57277980250893 chr3 198022430 9805763819 49.51845010183948 44.202238456864904 chr4 191154276 9996032535 52.29301035881614 321.74516747032123 chr5 180915260 8973127136 49.59850891516835 43.14599383410438 chr6 171115067 8550276096 49.96799081404094 205.8654142229609 chr7 159138663 7977295055 50.1279507105071 490.256172259398 chr8 146364022 7456184765 50.94274305334408 578.8278672032624 chr9 141213431 6222794011 44.06658748345262 590.8612538866641 chr10 135534747 7463893127 55.06996022946057 876.4037496661189 chr11 135006516 6671862058 49.418815148151815 295.37991540117326 chr12 133851895 6485070877 48.44960078450888 33.010197685305364 chr13 115169878 4801989808 41.69484149318974 24.591965710644438 chr14 107349540 4383974740 40.838318822791415 44.81805740835797 chr15 102531392 4044586708 39.44730125189366 24.318014386600677 chr16 90354753 4291882283 47.500348797367636 307.93986424972087 chr17 81195210 3869468859 47.65636863307577 302.99677722526445 chr18 78077248 4124331401 52.823729148342935 701.6222400328662 chr19 59128983 2632349312 44.51876522212466 510.47892409919945 chr20 63025520 2902441606 46.05184702958421 72.56007364817711 chr21 48129895 2023178977 42.03580699687793 138.33414022238782 chr22 51304566 1629175084 31.75497253012529 123.2899709215294 chrMT 16571 234482679 14150.182789210066 1909.9439695879462 chrX 155270560 3884760282 25.019297167473344 117.98190523631861 chrY 59373566 1329117986 22.38568567702334 339.2273846335023