BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,048,860 number of mapped reads = 3,338,326 (82.45%) number of supplementary alignments = 91 (0%) number of secondary alignments = 0 number of mapped bases = 166,467,685 bp number of sequenced bases = 166,452,111 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,984 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6 >>>>>>> ACTG content number of A's = 51,582,595 bp (30.99%) number of C's = 31,630,662 bp (19%) number of T's = 51,271,654 bp (30.8%) number of G's = 31,959,043 bp (19.2%) number of N's = 8,157 bp (0%) GC percentage = 38.2% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 264,127 number of insertions = 11,516 mapped reads with insertion percentage = 0.34% number of deletions = 9,056 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.0538X std coverageData = 0.2394X There is a 5.08% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 12013210 0.04819731221452002 0.2273759307006728 chr2 243199373 14734633 0.06058664057493273 0.25309134435059444 chr3 198022430 12627196 0.06376649352298121 0.2594785404609472 chr4 191154276 11887376 0.062187340240298886 0.2560908050878932 chr5 180915260 11418634 0.06311592510217215 0.25894734460749447 chr6 171115067 10739348 0.06276097241629809 0.25789879854524295 chr7 159138663 9331958 0.05864041977027292 0.249765125567011 chr8 146364022 8823735 0.06028622935764911 0.25236829019283674 chr9 141213431 7178183 0.05083215491025071 0.233347400715792 chr10 135534747 6725488 0.049621872979923 0.22874292341506935 chr11 135006516 7536895 0.05582615730932572 0.2443950410684679 chr12 133851895 7662691 0.057247534672557304 0.24690094421115114 chr13 115169878 6909452 0.0599935688045098 0.25301399415564557 chr14 107349540 5013845 0.04670578933081595 0.22356558535321192 chr15 102531392 4551490 0.04439118509187898 0.2180213960561021 chr16 90354753 3234263 0.035795161766420856 0.19481307152187732 chr17 81195210 2936468 0.03616553242488073 0.196597416785488 chr18 78077248 4675315 0.05988063257557438 0.2512806768010092 chr19 59128983 1481215 0.02505057460568872 0.16223568305427785 chr20 63025520 2725286 0.04324099190296248 0.21489293427828746 chr21 48129895 2022184 0.04201513425283807 0.21298699570283935 chr22 51304566 958059 0.018673951944160293 0.14078689588037543 chrMT 16571 50 0.003017319413433106 0.05484719862481972 chrX 155270560 11033224 0.07105805504919928 0.27520621473545515 chrY 59373566 247487 0.004168302776356738 0.06797887404849831