BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231752.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 = 5,508,495 number of mapped reads = 5,152,024 (93.53%) number of supplementary alignments = 35,716 (0.65%) number of secondary alignments = 0 number of mapped bases = 351,822,581 bp number of sequenced bases = 351,695,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 601,980 duplication rate = 5.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1784 >>>>>>> ACTG content number of A's = 92,186,488 bp (26.21%) number of C's = 65,073,811 bp (18.5%) number of T's = 100,341,868 bp (28.53%) number of G's = 94,017,608 bp (26.73%) number of N's = 75,591 bp (0.02%) GC percentage = 45.24% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,313,972 number of insertions = 24,419 mapped reads with insertion percentage = 0.47% number of deletions = 76,542 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 0.1136X std coverageData = 38.8126X There is a 6.76% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% 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 28249074 0.11333602254094284 1.5113468482244252 chr2 243199373 44529881 0.183100311693649 138.44519547046804 chr3 198022430 15096354 0.07623557593955392 0.39559747312507415 chr4 191154276 2334384 0.012212041754169288 0.2511708482332953 chr5 180915260 18551436 0.10254212939251227 0.47435533906644445 chr6 171115067 22077902 0.12902371712246707 0.772865249186359 chr7 159138663 24465464 0.15373676980056067 1.1193012922554033 chr8 146364022 21013104 0.14356741303542478 0.8485380870490573 chr9 141213431 13457034 0.0952957088054889 0.867478353777559 chr10 135534747 16996058 0.1254000053580356 0.7798777643189158 chr11 135006516 2191805 0.016234808992478554 0.5974120527084908 chr12 133851895 16515808 0.12338867522196828 0.5186854982941448 chr13 115169878 20182129 0.17523791246874465 0.6243758239876948 chr14 107349540 17295442 0.1611133312727749 0.742009869289776 chr15 102531392 9630117 0.09392359561450214 0.4456987813669882 chr16 90354753 10012663 0.11081501157996636 0.6105744887455469 chr17 81195210 15696575 0.19331897780669574 0.7103777249333445 chr18 78077248 13162950 0.1685888057939747 1.942839747379137 chr19 59128983 12100800 0.20465090698414345 1.0994232745010237 chr20 63025520 11641134 0.18470508454353093 0.6694776759112184 chr21 48129895 9395251 0.19520613955214322 0.7266607718671997 chr22 51304566 4845765 0.09445095003824806 0.4564860520683089 chrMT 16571 12091 0.7296481805563937 1.1575592335926488 chrX 155270560 1707109 0.010994415167949417 0.39140557656834823 chrY 59373566 662251 0.011153970438629203 0.2594086892218134