BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163154.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 90,915,068 number of mapped reads = 88,404,508 (97.24%) number of supplementary alignments = 410,048 (0.45%) number of secondary alignments = 0 number of mapped bases = 8,693,534,937 bp number of sequenced bases = 8,692,526,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,785,664 duplication rate = 43.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1101 >>>>>>> ACTG content number of A's = 2,158,246,915 bp (24.83%) number of C's = 2,181,123,600 bp (25.09%) number of T's = 2,164,057,643 bp (24.9%) number of G's = 2,174,575,768 bp (25.02%) number of N's = 14,522,341 bp (0.17%) GC percentage = 50.11% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 55,534,514 number of insertions = 603,147 mapped reads with insertion percentage = 0.67% number of deletions = 442,859 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 2.8083X std coverageData = 34.6438X There is a 10.52% of reference with a coverageData >= 1X There is a 6.61% of reference with a coverageData >= 2X There is a 5.01% of reference with a coverageData >= 3X There is a 4.43% of reference with a coverageData >= 4X There is a 4.02% of reference with a coverageData >= 5X There is a 3.75% of reference with a coverageData >= 6X There is a 3.53% of reference with a coverageData >= 7X There is a 3.35% of reference with a coverageData >= 8X There is a 3.2% of reference with a coverageData >= 9X There is a 3.07% of reference with a coverageData >= 10X There is a 2.95% of reference with a coverageData >= 11X There is a 2.84% of reference with a coverageData >= 12X There is a 2.74% of reference with a coverageData >= 13X There is a 2.65% of reference with a coverageData >= 14X There is a 2.57% of reference with a coverageData >= 15X There is a 2.49% of reference with a coverageData >= 16X There is a 2.42% of reference with a coverageData >= 17X There is a 2.35% of reference with a coverageData >= 18X There is a 2.29% of reference with a coverageData >= 19X There is a 2.23% of reference with a coverageData >= 20X There is a 2.18% of reference with a coverageData >= 21X There is a 2.12% of reference with a coverageData >= 22X There is a 2.07% of reference with a coverageData >= 23X There is a 2.03% of reference with a coverageData >= 24X There is a 1.98% of reference with a coverageData >= 25X There is a 1.94% of reference with a coverageData >= 26X There is a 1.9% of reference with a coverageData >= 27X There is a 1.86% of reference with a coverageData >= 28X There is a 1.82% of reference with a coverageData >= 29X There is a 1.78% of reference with a coverageData >= 30X There is a 1.75% of reference with a coverageData >= 31X There is a 1.71% of reference with a coverageData >= 32X There is a 1.68% of reference with a coverageData >= 33X There is a 1.65% of reference with a coverageData >= 34X There is a 1.62% of reference with a coverageData >= 35X There is a 1.59% of reference with a coverageData >= 36X There is a 1.56% of reference with a coverageData >= 37X There is a 1.53% of reference with a coverageData >= 38X There is a 1.51% of reference with a coverageData >= 39X There is a 1.48% of reference with a coverageData >= 40X There is a 1.46% of reference with a coverageData >= 41X There is a 1.43% of reference with a coverageData >= 42X There is a 1.41% of reference with a coverageData >= 43X There is a 1.39% of reference with a coverageData >= 44X There is a 1.36% of reference with a coverageData >= 45X There is a 1.34% of reference with a coverageData >= 46X There is a 1.32% of reference with a coverageData >= 47X There is a 1.3% of reference with a coverageData >= 48X There is a 1.28% of reference with a coverageData >= 49X There is a 1.26% of reference with a coverageData >= 50X There is a 1.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 939181861 3.7680221506850327 37.65217767877438 chr2 243199373 571622475 2.3504274207154308 26.006146163382844 chr3 198022430 415393306 2.097708355563559 24.062940050734586 chr4 191154276 301406246 1.5767695722380806 21.774924133338136 chr5 180915260 432520970 2.390737906796806 33.65235661185532 chr6 171115067 415138683 2.4260790722771364 29.290530782185158 chr7 159138663 400861761 2.5189463920530737 33.53526109865696 chr8 146364022 484014295 3.306921252819904 73.14550360789511 chr9 141213431 409044364 2.8966392297344576 33.52114053151275 chr10 135534747 355343588 2.6217895843344143 26.889209069215852 chr11 135006516 464757111 3.442479109674973 30.53008496208886 chr12 133851895 404515062 3.022109339580138 34.03094841498314 chr13 115169878 166710234 1.4475159381518143 19.79333174460711 chr14 107349540 199918061 1.862309433277497 20.401775274981137 chr15 102531392 337725211 3.2938713150407635 32.56478465603222 chr16 90354753 365675280 4.04710618820462 35.77000352421786 chr17 81195210 459556921 5.65990187105865 49.65928640235479 chr18 78077248 128560317 1.6465784885245955 19.119920854856204 chr19 59128983 522794773 8.841599271206812 58.750361017391164 chr20 63025520 209240413 3.319931561056537 36.428967858913936 chr21 48129895 107456121 2.2326273722392287 33.56395294566066 chr22 51304566 150696702 2.9372961073289265 31.487859534263897 chrMT 16571 914 0.05515659887755718 0.2780991527749019 chrX 155270560 442559881 2.850249789786293 35.54876731219341 chrY 59373566 8840387 0.1488943244540845 8.607022769951755