BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085036.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 = 2,761,718 number of mapped reads = 2,509,769 (90.88%) number of supplementary alignments = 16,942 (0.61%) number of secondary alignments = 0 number of mapped bases = 167,798,957 bp number of sequenced bases = 167,739,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,094 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7212 >>>>>>> ACTG content number of A's = 46,613,345 bp (27.79%) number of C's = 32,756,612 bp (19.53%) number of T's = 50,884,341 bp (30.34%) number of G's = 37,465,837 bp (22.34%) number of N's = 18,926 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,473,178 number of insertions = 12,275 mapped reads with insertion percentage = 0.48% number of deletions = 34,682 mapped reads with deletion percentage = 1.37% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.4058X There is a 4.56% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14569447 0.05845300180816801 0.561126600077127 chr2 243199373 17167849 0.07059166636913985 0.5704905524305265 chr3 198022430 10283569 0.05193133424329759 0.2624895157299539 chr4 191154276 9522178 0.04981409884861796 0.2669752643483793 chr5 180915260 7744830 0.04280915827664289 0.23696260241310038 chr6 171115067 12746055 0.07448820973783682 0.4721563753702002 chr7 159138663 13260621 0.08332746266694474 0.434116878424282 chr8 146364022 10565310 0.07218515763388901 0.6503160917763204 chr9 141213431 6036804 0.04274950305541404 0.384837792009053 chr10 135534747 11752728 0.08671376351925458 0.508109244435262 chr11 135006516 5734782 0.042477816404061564 0.3627751812387562 chr12 133851895 7305672 0.054580265748198784 0.27567395745259793 chr13 115169878 2923515 0.02538437177123692 0.18023673409556426 chr14 107349540 5788564 0.053922578522460365 0.28199284524116097 chr15 102531392 3050779 0.029754584820227546 0.20584428459132256 chr16 90354753 4461640 0.049379140021554815 0.2783542447885625 chr17 81195210 3096408 0.03813535305838854 0.24564400702603886 chr18 78077248 4018251 0.05146506956802576 0.6827109468448753 chr19 59128983 2777540 0.0469742562627874 0.43256204022252187 chr20 63025520 4256306 0.06753305645078375 0.30351206022596766 chr21 48129895 1902393 0.039526223774225974 0.2422119250778448 chr22 51304566 1229021 0.023955392196476237 0.17403339722581404 chrMT 16571 10292 0.6210850280610706 0.9935533881572123 chrX 155270560 7248384 0.04668228156065129 0.28407830151745106 chrY 59373566 346019 0.005827829172328979 0.13477326515505542