BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618674.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 = 209,825,172 number of mapped reads = 203,234,848 (96.86%) number of supplementary alignments = 514,340 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 101,585,984 number of mapped paired reads (second in pair) = 101,648,864 number of mapped paired reads (both in pair) = 200,452,356 number of mapped paired reads (singletons) = 2,782,492 number of mapped bases = 19,667,383,171 bp number of sequenced bases = 19,661,808,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,309,868 duplication rate = 10.47% >>>>>>> Insert size mean insert size = 38,030.2931 std insert size = 1,872,417.0883 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 53.6046 >>>>>>> ACTG content number of A's = 5,750,638,249 bp (29.25%) number of C's = 4,105,119,858 bp (20.88%) number of T's = 5,723,286,737 bp (29.11%) number of G's = 4,081,608,931 bp (20.76%) number of N's = 1,154,992 bp (0.01%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 213,292,748 number of insertions = 2,237,627 mapped reads with insertion percentage = 1.07% number of deletions = 2,465,448 mapped reads with deletion percentage = 1.18% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 6.3531X std coverageData = 60.3815X There is a 91.05% of reference with a coverageData >= 1X There is a 89.25% of reference with a coverageData >= 2X There is a 85.17% of reference with a coverageData >= 3X There is a 78.05% of reference with a coverageData >= 4X There is a 68.04% of reference with a coverageData >= 5X There is a 56.14% of reference with a coverageData >= 6X There is a 43.8% of reference with a coverageData >= 7X There is a 32.36% of reference with a coverageData >= 8X There is a 22.73% of reference with a coverageData >= 9X There is a 15.25% of reference with a coverageData >= 10X There is a 9.84% of reference with a coverageData >= 11X There is a 6.15% of reference with a coverageData >= 12X There is a 3.77% of reference with a coverageData >= 13X There is a 2.29% of reference with a coverageData >= 14X There is a 1.41% of reference with a coverageData >= 15X There is a 0.9% of reference with a coverageData >= 16X There is a 0.6% of reference with a coverageData >= 17X There is a 0.43% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1598701157 6.414030787911257 151.24453412216107 chr2 243199373 1662720563 6.836862046515227 35.36587067766187 chr3 198022430 1291821796 6.5236134916635455 4.447284340940796 chr4 191154276 1302843689 6.81566594408801 51.36240143652722 chr5 180915260 1174162432 6.4901237850251 5.109697383423659 chr6 171115067 1133829237 6.62612157350235 40.32083524419579 chr7 159138663 1059719735 6.659096633229852 45.394823878446786 chr8 146364022 977977671 6.681817414118341 37.27571323614836 chr9 141213431 832030441 5.892006412619491 60.85959951778267 chr10 135534747 1013399340 7.477044539729727 124.44368861671504 chr11 135006516 895202083 6.630806493813973 27.9273327996305 chr12 133851895 866389535 6.472747621540957 5.389076792086709 chr13 115169878 624415696 5.421692779773545 4.05284403268035 chr14 107349540 589113959 5.48781074422862 5.425221759381247 chr15 102531392 553275751 5.396159558625714 4.08160251849367 chr16 90354753 606211310 6.709235428932001 37.56826069890282 chr17 81195210 546310181 6.728354800732704 30.574374639008656 chr18 78077248 550743994 7.053834607490264 87.86680501432355 chr19 59128983 393312182 6.651766393479151 62.37046887353816 chr20 63025520 411149811 6.5235449227551 15.602922837064165 chr21 48129895 268757796 5.584009605672317 18.42670270000718 chr22 51304566 239844166 4.674908779074362 4.887536598097077 chrMT 16571 5839833 352.41282964214594 41.94781208410622 chrX 155270560 1011980438 6.517529388700601 16.290314124706025 chrY 59373566 57630375 0.9706402846007262 42.171469929577505