BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618646.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 101,279,821 number of mapped reads = 95,490,822 (94.28%) number of supplementary alignments = 337,347 (0.33%) number of secondary alignments = 0 number of mapped bases = 9,195,162,934 bp number of sequenced bases = 9,188,077,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,235,377 duplication rate = 63.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.6069 >>>>>>> ACTG content number of A's = 2,461,898,581 bp (26.79%) number of C's = 2,159,940,082 bp (23.51%) number of T's = 2,786,315,067 bp (30.33%) number of G's = 1,779,478,688 bp (19.37%) number of N's = 445,387 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 82,327,233 number of insertions = 1,785,907 mapped reads with insertion percentage = 1.83% number of deletions = 4,305,414 mapped reads with deletion percentage = 4.39% homopolymer indels = 50.17% >>>>>>> Coverage mean coverageData = 2.9703X std coverageData = 91.7895X There is a 14.15% of reference with a coverageData >= 1X There is a 10.38% of reference with a coverageData >= 2X There is a 8.7% of reference with a coverageData >= 3X There is a 7.65% of reference with a coverageData >= 4X There is a 6.88% of reference with a coverageData >= 5X There is a 6.26% of reference with a coverageData >= 6X There is a 5.71% of reference with a coverageData >= 7X There is a 5.22% of reference with a coverageData >= 8X There is a 4.78% of reference with a coverageData >= 9X There is a 4.39% of reference with a coverageData >= 10X There is a 4.05% of reference with a coverageData >= 11X There is a 3.75% of reference with a coverageData >= 12X There is a 3.5% of reference with a coverageData >= 13X There is a 3.28% of reference with a coverageData >= 14X There is a 3.09% of reference with a coverageData >= 15X There is a 2.92% of reference with a coverageData >= 16X There is a 2.77% of reference with a coverageData >= 17X There is a 2.63% of reference with a coverageData >= 18X There is a 2.5% of reference with a coverageData >= 19X There is a 2.39% of reference with a coverageData >= 20X There is a 2.28% of reference with a coverageData >= 21X There is a 2.18% of reference with a coverageData >= 22X There is a 2.09% of reference with a coverageData >= 23X There is a 2.01% of reference with a coverageData >= 24X There is a 1.94% of reference with a coverageData >= 25X There is a 1.86% of reference with a coverageData >= 26X There is a 1.8% of reference with a coverageData >= 27X There is a 1.74% of reference with a coverageData >= 28X There is a 1.68% of reference with a coverageData >= 29X There is a 1.63% of reference with a coverageData >= 30X There is a 1.58% of reference with a coverageData >= 31X There is a 1.53% of reference with a coverageData >= 32X There is a 1.48% of reference with a coverageData >= 33X There is a 1.44% of reference with a coverageData >= 34X There is a 1.4% of reference with a coverageData >= 35X There is a 1.36% of reference with a coverageData >= 36X There is a 1.33% of reference with a coverageData >= 37X There is a 1.29% of reference with a coverageData >= 38X There is a 1.26% of reference with a coverageData >= 39X There is a 1.23% of reference with a coverageData >= 40X There is a 1.2% of reference with a coverageData >= 41X There is a 1.17% of reference with a coverageData >= 42X There is a 1.14% of reference with a coverageData >= 43X There is a 1.12% of reference with a coverageData >= 44X There is a 1.09% of reference with a coverageData >= 45X There is a 1.07% of reference with a coverageData >= 46X There is a 1.04% of reference with a coverageData >= 47X There is a 1.02% of reference with a coverageData >= 48X There is a 1% of reference with a coverageData >= 49X There is a 0.98% of reference with a coverageData >= 50X There is a 0.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 893791194 3.5859136094188506 59.66912602242602 chr2 243199373 779537453 3.2053431856504004 115.23758461983932 chr3 198022430 608701669 3.0739026331512043 47.800323245335996 chr4 191154276 540046677 2.8251875307251826 209.75501188758508 chr5 180915260 529288780 2.925617109358271 53.98581760087684 chr6 171115067 558717360 3.265155838088764 46.199568299070314 chr7 159138663 499628502 3.1395796130321894 58.49787005454184 chr8 146364022 435173024 2.973224007194883 52.89031775867427 chr9 141213431 403072786 2.8543516232531734 44.945244085602184 chr10 135534747 459510484 3.3903518778103447 79.53227597425726 chr11 135006516 525911502 3.8954527350368777 63.556535650992075 chr12 133851895 426243778 3.184443358086189 235.65482363921905 chr13 115169878 281614679 2.445211229623774 42.398021502254835 chr14 107349540 272098163 2.5346933298456613 38.461455213703594 chr15 102531392 291621807 2.844219719556719 45.160608316676324 chr16 90354753 373300938 4.13150305441043 75.36760300141304 chr17 81195210 257784654 3.1748751434967653 45.288294516759656 chr18 78077248 245271213 3.1413916253810585 46.411380960599075 chr19 59128983 182040789 3.078706579478967 51.99545395604917 chr20 63025520 260094916 4.126819040921836 48.35329732486124 chr21 48129895 118921272 2.470840046503322 49.20800295751846 chr22 51304566 141167556 2.751559305657122 45.476082040185275 chrMT 16571 28090 1.695130046466719 8.335522315980711 chrX 155270560 19221948 0.12379647500466283 11.4261294507075 chrY 59373566 92373700 1.5558051540983744 51.881898984131595