BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081179.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,732,776 number of mapped reads = 2,481,785 (90.82%) number of supplementary alignments = 27,762 (1.02%) number of secondary alignments = 0 number of mapped bases = 167,341,456 bp number of sequenced bases = 167,279,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,398 duplication rate = 3.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2091 >>>>>>> ACTG content number of A's = 47,784,525 bp (28.57%) number of C's = 30,765,363 bp (18.39%) number of T's = 52,875,906 bp (31.61%) number of G's = 35,804,295 bp (21.4%) number of N's = 49,341 bp (0.03%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,362,886 number of insertions = 13,228 mapped reads with insertion percentage = 0.53% number of deletions = 38,341 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.4191X There is a 4.56% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13992664 0.05613893335094238 0.7969876167240502 chr2 243199373 14011705 0.057614067121793115 0.4688261956188553 chr3 198022430 11430918 0.05772536979775473 0.2745193386219253 chr4 191154276 10671983 0.05582916178134566 0.27884743379488697 chr5 180915260 10927521 0.06040132269660392 0.28279036057257706 chr6 171115067 10017092 0.058540093374711416 0.3369103489555158 chr7 159138663 8623539 0.0541888365619862 0.4632829727905623 chr8 146364022 8660272 0.059169404349929657 0.5747304739862675 chr9 141213431 7199740 0.05098481036127506 0.3618367667648061 chr10 135534747 7443292 0.054917961369714295 0.36382657983256894 chr11 135006516 7602592 0.05631277826619865 0.3812016264348853 chr12 133851895 7157609 0.0534740953798226 0.26672120709950403 chr13 115169878 5448888 0.04731174587160716 0.24860927313982123 chr14 107349540 5329983 0.04965072975627096 0.26423673056824365 chr15 102531392 4832948 0.047136276078257086 0.25246786364541557 chr16 90354753 4141646 0.04583761077848334 0.27698689194759823 chr17 81195210 4297235 0.052924735338451614 0.29617922886629966 chr18 78077248 4374477 0.05602755107352144 0.7089563510418295 chr19 59128983 2779128 0.047001112804527685 0.5545825693161105 chr20 63025520 3395908 0.05388147531349206 0.2697681082630457 chr21 48129895 2215560 0.0460329281832009 0.2573219178164212 chr22 51304566 1560845 0.03042312062439043 0.19690499403888653 chrMT 16571 16506 0.996077484762537 1.237372542903079 chrX 155270560 10811433 0.06962963874156182 0.32619434703231515 chrY 59373566 397972 0.006702848200156952 0.1277666412140327