BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124898.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,258,960 number of mapped reads = 6,180,016 (98.74%) number of supplementary alignments = 32,741 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,091,643 number of mapped paired reads (second in pair) = 3,088,373 number of mapped paired reads (both in pair) = 6,154,668 number of mapped paired reads (singletons) = 25,348 number of mapped bases = 564,813,000 bp number of sequenced bases = 564,502,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 427,739 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 62,206.0695 std insert size = 2,346,386.2771 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 52.8276 >>>>>>> ACTG content number of A's = 161,387,246 bp (28.59%) number of C's = 110,560,617 bp (19.59%) number of T's = 169,680,431 bp (30.06%) number of G's = 122,864,625 bp (21.77%) number of N's = 9,807 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 4,390,329 number of insertions = 95,821 mapped reads with insertion percentage = 1.51% number of deletions = 176,029 mapped reads with deletion percentage = 2.79% homopolymer indels = 45.47% >>>>>>> Coverage mean coverageData = 0.1825X std coverageData = 2.6256X There is a 12.08% of reference with a coverageData >= 1X There is a 3.67% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 45814132 0.18380749390389683 3.1303301346826813 chr2 243199373 51626853 0.21228201521720205 2.40045920370696 chr3 198022430 39486935 0.19940637532828984 0.7413899390403172 chr4 191154276 32469993 0.16986276048567178 1.9622003925776286 chr5 180915260 33464075 0.1849709913912182 0.5758614222779677 chr6 171115067 29155694 0.17038648034424694 1.946062984953388 chr7 159138663 30842807 0.19381089685289113 2.6487558847300563 chr8 146364022 27454835 0.18757912378220926 0.8656791538949138 chr9 141213431 24381216 0.1726550783968984 2.9570172967532815 chr10 135534747 32396115 0.23902442522728137 8.362593690710987 chr11 135006516 27057201 0.2004140377935536 1.6319730491892488 chr12 133851895 25747959 0.1923615575259506 0.5769553112756389 chr13 115169878 17600781 0.15282451718842666 0.5024435451688617 chr14 107349540 16727283 0.1558207235913633 0.6178685087514137 chr15 102531392 15471528 0.1508955228072979 0.5037956835673323 chr16 90354753 21611696 0.23918715156025053 4.549481790534766 chr17 81195210 12213485 0.1504212502190708 1.4099951366229588 chr18 78077248 16168222 0.20707981408361115 3.1610888844237435 chr19 59128983 7635751 0.12913719486770134 1.6593938055488542 chr20 63025520 11752207 0.18646743414413716 0.7137669452793796 chr21 48129895 7110708 0.14773994416567915 0.8860154825212262 chr22 51304566 5438508 0.10600436616109374 0.4580652157252147 chrMT 16571 74424 4.49121960050691 3.5265758615463 chrX 155270560 31149205 0.20061243419228988 1.0547307848028793 chrY 59373566 1961387 0.033034684155571856 2.143172359882189