BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472386.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,483,750 number of mapped reads = 20,268,067 (98.95%) number of supplementary alignments = 77,022 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,189,589 number of mapped paired reads (second in pair) = 10,078,478 number of mapped paired reads (both in pair) = 20,113,808 number of mapped paired reads (singletons) = 154,259 number of mapped bases = 1,991,615,696 bp number of sequenced bases = 1,991,372,378 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,909,999 duplication rate = 48.1% >>>>>>> Insert size mean insert size = 20,125.3441 std insert size = 1,420,066.695 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 54.9301 >>>>>>> ACTG content number of A's = 536,689,364 bp (26.95%) number of C's = 460,327,335 bp (23.12%) number of T's = 537,230,957 bp (26.98%) number of G's = 456,874,897 bp (22.94%) number of N's = 249,825 bp (0.01%) GC percentage = 46.06% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 11,295,503 number of insertions = 119,221 mapped reads with insertion percentage = 0.58% number of deletions = 100,216 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.8% >>>>>>> Coverage mean coverageData = 0.6434X std coverageData = 19.5071X There is a 5.25% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.23% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194258806 0.7793714022481814 23.023614170900583 chr2 243199373 184183941 0.7573372362271674 25.083756960599207 chr3 198022430 141568956 0.714913739822302 15.209226782761757 chr4 191154276 40576217 0.21226947075983799 7.207326218490688 chr5 180915260 63862910 0.35299902285744167 10.3235248987306 chr6 171115067 153289087 0.8958246032186049 19.281337464031115 chr7 159138663 161274350 1.0134202899517888 33.09446589337619 chr8 146364022 88870200 0.607186102059972 16.37050350643191 chr9 141213431 70258824 0.4975364135157937 12.070016098769926 chr10 135534747 51588593 0.3806300165964083 10.597972787554742 chr11 135006516 52857647 0.3915192285978256 13.185888245593366 chr12 133851895 106794239 0.7978537696459209 23.078387748784007 chr13 115169878 52472075 0.45560589201978663 12.866497900450286 chr14 107349540 29204470 0.27205025750459666 6.800223460472817 chr15 102531392 32655860 0.3184962123600156 10.927575162284228 chr16 90354753 82722089 0.915525594984472 21.62571694874691 chr17 81195210 129461472 1.5944471601218841 34.54709865211747 chr18 78077248 25661135 0.32866341549333294 11.791045237259638 chr19 59128983 50713478 0.8576754651775425 17.7087722983774 chr20 63025520 85804664 1.3614273075414531 34.30648726402302 chr21 48129895 17942904 0.3728016443833921 22.857677050004753 chr22 51304566 18381314 0.35827832555878164 9.91961790533116 chrMT 16571 13197 0.796391285981534 1.2575376579924187 chrX 155270560 156824535 1.010008175406851 25.45387436645992 chrY 59373566 374733 0.006311445062942657 0.40365005779232654