BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472713.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,551,680 number of mapped reads = 17,395,378 (99.11%) number of supplementary alignments = 61,993 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,730,158 number of mapped paired reads (second in pair) = 8,665,220 number of mapped paired reads (both in pair) = 17,295,660 number of mapped paired reads (singletons) = 99,718 number of mapped bases = 1,710,556,395 bp number of sequenced bases = 1,710,288,018 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,011,414 duplication rate = 46.13% >>>>>>> Insert size mean insert size = 23,258.7277 std insert size = 1,541,578.913 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 55.1595 >>>>>>> ACTG content number of A's = 465,311,429 bp (27.21%) number of C's = 392,578,377 bp (22.95%) number of T's = 461,716,624 bp (27%) number of G's = 390,349,846 bp (22.82%) number of N's = 331,742 bp (0.02%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,006,711 number of insertions = 102,686 mapped reads with insertion percentage = 0.58% number of deletions = 93,245 mapped reads with deletion percentage = 0.53% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.5526X std coverageData = 19.3389X There is a 5.17% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196740200 0.7893268197714942 27.563881066253177 chr2 243199373 113791546 0.4678940763552051 15.009766749561116 chr3 198022430 159169102 0.8037932975572515 19.148837884434055 chr4 191154276 69075372 0.36135928238403625 13.413387277453943 chr5 180915260 87773183 0.48516185422943314 14.97927647065039 chr6 171115067 113460119 0.6630632882842514 16.90854103730332 chr7 159138663 79488314 0.4994908999581076 17.881351945941717 chr8 146364022 68834127 0.4702940385171979 16.87757908738099 chr9 141213431 94417643 0.668616592142712 16.38960570475997 chr10 135534747 49550138 0.36558992506917803 18.067998063888126 chr11 135006516 94323965 0.6986623149359694 26.399795947091135 chr12 133851895 84783551 0.6334131541432417 19.665851097828522 chr13 115169878 39066549 0.3392080436170993 13.89976262011449 chr14 107349540 40617946 0.3783709366616755 20.005189262401835 chr15 102531392 45889484 0.44756521007731953 17.978955076892717 chr16 90354753 58874661 0.6515945099202474 18.401947332504843 chr17 81195210 75618718 0.9313199387008174 25.29265174138902 chr18 78077248 41177047 0.5273885549859544 26.844949995672458 chr19 59128983 35814048 0.6056936240557359 16.036545608357386 chr20 63025520 44605311 0.7077341210354154 22.854118378433604 chr21 48129895 9306978 0.1933720819461584 9.601512429486634 chr22 51304566 14476136 0.28216077298071285 8.292015510880807 chrMT 16571 1245 0.07513125339448434 0.31338702744967173 chrX 155270560 90665867 0.583921813639366 25.732238768377524 chrY 59373566 3035145 0.05111946619477092 2.282947227368711