BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153313.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 = 183,203,526 number of mapped reads = 177,189,650 (96.72%) number of supplementary alignments = 1,062,290 (0.58%) number of secondary alignments = 0 number of mapped bases = 17,488,896,202 bp number of sequenced bases = 17,486,966,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,665,973 duplication rate = 52.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6049 >>>>>>> ACTG content number of A's = 4,006,275,702 bp (22.91%) number of C's = 4,737,197,452 bp (27.09%) number of T's = 4,028,958,512 bp (23.04%) number of G's = 4,694,214,602 bp (26.84%) number of N's = 20,320,707 bp (0.12%) GC percentage = 53.93% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 111,340,558 number of insertions = 712,397 mapped reads with insertion percentage = 0.39% number of deletions = 791,678 mapped reads with deletion percentage = 0.44% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 5.6494X std coverageData = 63.4686X There is a 14.8% of reference with a coverageData >= 1X There is a 9.23% of reference with a coverageData >= 2X There is a 6.76% of reference with a coverageData >= 3X There is a 5.92% of reference with a coverageData >= 4X There is a 5.35% of reference with a coverageData >= 5X There is a 5.01% of reference with a coverageData >= 6X There is a 4.76% of reference with a coverageData >= 7X There is a 4.56% of reference with a coverageData >= 8X There is a 4.39% of reference with a coverageData >= 9X There is a 4.25% of reference with a coverageData >= 10X There is a 4.12% of reference with a coverageData >= 11X There is a 4.01% of reference with a coverageData >= 12X There is a 3.91% of reference with a coverageData >= 13X There is a 3.81% of reference with a coverageData >= 14X There is a 3.73% of reference with a coverageData >= 15X There is a 3.64% of reference with a coverageData >= 16X There is a 3.57% of reference with a coverageData >= 17X There is a 3.5% of reference with a coverageData >= 18X There is a 3.43% of reference with a coverageData >= 19X There is a 3.36% of reference with a coverageData >= 20X There is a 3.3% of reference with a coverageData >= 21X There is a 3.24% of reference with a coverageData >= 22X There is a 3.19% of reference with a coverageData >= 23X There is a 3.13% of reference with a coverageData >= 24X There is a 3.08% of reference with a coverageData >= 25X There is a 3.03% of reference with a coverageData >= 26X There is a 2.98% of reference with a coverageData >= 27X There is a 2.94% of reference with a coverageData >= 28X There is a 2.89% of reference with a coverageData >= 29X There is a 2.85% of reference with a coverageData >= 30X There is a 2.81% of reference with a coverageData >= 31X There is a 2.77% of reference with a coverageData >= 32X There is a 2.73% of reference with a coverageData >= 33X There is a 2.69% of reference with a coverageData >= 34X There is a 2.65% of reference with a coverageData >= 35X There is a 2.62% of reference with a coverageData >= 36X There is a 2.58% of reference with a coverageData >= 37X There is a 2.55% of reference with a coverageData >= 38X There is a 2.51% of reference with a coverageData >= 39X There is a 2.48% of reference with a coverageData >= 40X There is a 2.45% of reference with a coverageData >= 41X There is a 2.42% of reference with a coverageData >= 42X There is a 2.39% of reference with a coverageData >= 43X There is a 2.36% of reference with a coverageData >= 44X There is a 2.33% of reference with a coverageData >= 45X There is a 2.3% of reference with a coverageData >= 46X There is a 2.28% of reference with a coverageData >= 47X There is a 2.25% of reference with a coverageData >= 48X There is a 2.22% of reference with a coverageData >= 49X There is a 2.2% of reference with a coverageData >= 50X There is a 2.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1678360686 6.733626898365882 57.179108611168964 chr2 243199373 817161593 3.360048107525343 31.980765814913678 chr3 198022430 750684735 3.790907600719777 36.770870767290994 chr4 191154276 429697247 2.2479081085269574 40.93955842102888 chr5 180915260 956575255 5.287421608326461 104.12638270776118 chr6 171115067 418646273 2.4465775009748265 25.304709139963606 chr7 159138663 954245100 5.9963121595410165 88.82277658656582 chr8 146364022 964913941 6.5925623511493825 110.48457898622233 chr9 141213431 417410928 2.955886880193429 26.532397645829363 chr10 135534747 731304365 5.3956965367707515 47.28626648934316 chr11 135006516 908587619 6.729953826821218 54.1192266388268 chr12 133851895 746284892 5.575452570170934 43.44338002170607 chr13 115169878 114802839 0.9968130642632095 12.042213524388313 chr14 107349540 404236880 3.7656135275474867 35.664682783089454 chr15 102531392 959878189 9.361798082288788 72.34717448245672 chr16 90354753 1162114801 12.861689755269433 96.02165557137026 chr17 81195210 1211768943 14.924143222241804 93.88903186558734 chr18 78077248 108778640 1.3932181626073705 14.321981296582122 chr19 59128983 1635617719 27.66186117221059 128.02023076812011 chr20 63025520 517978106 8.218545535205422 60.79370446233692 chr21 48129895 224018971 4.654466231434745 92.67593770234726 chr22 51304566 583791868 11.37894564783961 89.07331327216376 chrMT 16571 3274 0.19757407519159978 0.5410627759449808 chrX 155270560 775274912 4.993058001465313 44.229005850071964 chrY 59373566 16758426 0.28225399161640385 16.53980126459072