BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438299.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 873,783,930 number of mapped reads = 861,604,280 (98.61%) number of supplementary alignments = 3,063,786 (0.35%) number of secondary alignments = 0 number of mapped bases = 120,786,533,808 bp number of sequenced bases = 120,748,429,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 256,800,481 duplication rate = 25.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5279 >>>>>>> ACTG content number of A's = 36,105,592,654 bp (29.9%) number of C's = 24,362,791,813 bp (20.18%) number of T's = 35,925,366,224 bp (29.75%) number of G's = 24,354,048,945 bp (20.17%) number of N's = 630,059 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 479,139,542 number of insertions = 12,394,604 mapped reads with insertion percentage = 1.37% number of deletions = 13,648,186 mapped reads with deletion percentage = 1.51% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 39.0176X std coverageData = 359.3236X There is a 91.75% of reference with a coverageData >= 1X There is a 91.7% of reference with a coverageData >= 2X There is a 91.67% of reference with a coverageData >= 3X There is a 91.65% of reference with a coverageData >= 4X There is a 91.62% of reference with a coverageData >= 5X There is a 91.6% of reference with a coverageData >= 6X There is a 91.57% of reference with a coverageData >= 7X There is a 91.54% of reference with a coverageData >= 8X There is a 91.51% of reference with a coverageData >= 9X There is a 91.48% of reference with a coverageData >= 10X There is a 91.44% of reference with a coverageData >= 11X There is a 91.39% of reference with a coverageData >= 12X There is a 91.34% of reference with a coverageData >= 13X There is a 91.27% of reference with a coverageData >= 14X There is a 91.19% of reference with a coverageData >= 15X There is a 91.1% of reference with a coverageData >= 16X There is a 90.98% of reference with a coverageData >= 17X There is a 90.84% of reference with a coverageData >= 18X There is a 90.66% of reference with a coverageData >= 19X There is a 90.44% of reference with a coverageData >= 20X There is a 90.16% of reference with a coverageData >= 21X There is a 89.81% of reference with a coverageData >= 22X There is a 89.37% of reference with a coverageData >= 23X There is a 88.81% of reference with a coverageData >= 24X There is a 88.12% of reference with a coverageData >= 25X There is a 87.25% of reference with a coverageData >= 26X There is a 86.18% of reference with a coverageData >= 27X There is a 84.89% of reference with a coverageData >= 28X There is a 83.34% of reference with a coverageData >= 29X There is a 81.52% of reference with a coverageData >= 30X There is a 79.41% of reference with a coverageData >= 31X There is a 76.99% of reference with a coverageData >= 32X There is a 74.27% of reference with a coverageData >= 33X There is a 71.27% of reference with a coverageData >= 34X There is a 67.99% of reference with a coverageData >= 35X There is a 64.46% of reference with a coverageData >= 36X There is a 60.74% of reference with a coverageData >= 37X There is a 56.85% of reference with a coverageData >= 38X There is a 52.86% of reference with a coverageData >= 39X There is a 48.8% of reference with a coverageData >= 40X There is a 44.75% of reference with a coverageData >= 41X There is a 40.74% of reference with a coverageData >= 42X There is a 36.84% of reference with a coverageData >= 43X There is a 33.07% of reference with a coverageData >= 44X There is a 29.48% of reference with a coverageData >= 45X There is a 26.11% of reference with a coverageData >= 46X There is a 22.97% of reference with a coverageData >= 47X There is a 20.07% of reference with a coverageData >= 48X There is a 17.43% of reference with a coverageData >= 49X There is a 15.05% of reference with a coverageData >= 50X There is a 12.92% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9780684497 39.24036159974101 853.3502953316795 chr2 243199373 10321499384 42.44048517345478 257.2701858979885 chr3 198022430 8008662243 40.44320758512053 62.79687155246045 chr4 191154276 7923076528 41.448596880982144 128.31681773006403 chr5 180915260 7328318967 40.50691449134805 30.38428760051111 chr6 171115067 6972115666 40.745188534449746 115.36381814113555 chr7 159138663 6525561509 41.00550668193059 295.0005481658713 chr8 146364022 6069716724 41.470004998906084 496.9756360160708 chr9 141213431 5263817762 37.275616948928885 354.7201062085171 chr10 135534747 6111855793 45.09438301456379 751.1465587218333 chr11 135006516 5475356052 40.55623546347941 175.16047631706442 chr12 133851895 5356745026 40.019941637733254 26.25653294264508 chr13 115169878 3872671356 33.625731165574386 21.69554895970737 chr14 107349540 3628611145 33.80183226681735 31.267996902570182 chr15 102531392 3330518122 32.48291139946681 20.630437243263437 chr16 90354753 3707126389 41.0285708932213 274.23831785309244 chr17 81195210 3275579879 40.34203346478198 187.92996366957334 chr18 78077248 3290074735 42.138712868056004 432.27715366436763 chr19 59128983 2331782908 39.43553211459768 444.98934096587135 chr20 63025520 2450977424 38.88865056567562 59.21198136583304 chr21 48129895 1645377807 34.18619149283413 101.93591518602372 chr22 51304566 1403959213 27.36519032243641 31.26393020644885 chrMT 16571 289091386 17445.621024681674 2160.809973855003 chrX 155270560 6068295981 39.08207699514963 105.5508735940597 chrY 59373566 355057312 5.980057050977871 238.83204302978643