BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536742.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 18,958,304 number of mapped reads = 15,416,657 (81.32%) number of supplementary alignments = 393 (0%) number of secondary alignments = 0 number of mapped bases = 768,551,404 bp number of sequenced bases = 768,484,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,292 duplication rate = 0.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3946 >>>>>>> ACTG content number of A's = 242,000,349 bp (31.49%) number of C's = 141,653,266 bp (18.43%) number of T's = 241,123,697 bp (31.38%) number of G's = 143,690,617 bp (18.7%) number of N's = 16,268 bp (0%) GC percentage = 37.13% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 2,654,453 number of insertions = 53,645 mapped reads with insertion percentage = 0.35% number of deletions = 39,761 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 0.2483X std coverageData = 0.7271X There is a 19.99% of reference with a coverageData >= 1X There is a 3.95% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.02% 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 57521952 0.2307795734639313 0.5371886312258473 chr2 243199373 72558529 0.2983499838217099 0.5977285950769964 chr3 198022430 63223394 0.3192739024564035 0.6158365597330926 chr4 191154276 67967822 0.3555652712681143 0.6487340852136249 chr5 180915260 57016842 0.3151577263299956 0.6120172637965259 chr6 171115067 52629319 0.3075668316221388 2.0968208735997353 chr7 159138663 44839591 0.28176428125451825 0.5889877356273983 chr8 146364022 43615657 0.29799438689926133 0.596053358002012 chr9 141213431 31676615 0.22431729599431657 0.5303220831698509 chr10 135534747 31815769 0.23474252694772066 0.5256619513312845 chr11 135006516 35117991 0.2601207115069913 0.562991761119238 chr12 133851895 34884761 0.2606220927989103 0.5745714875603585 chr13 115169878 34712310 0.30140094443791976 0.6099209837836063 chr14 107349540 23900592 0.22264270531573774 0.5255639338981847 chr15 102531392 18530230 0.18072738152233417 0.46981529563262014 chr16 90354753 12298015 0.13610811375910684 0.405247427071628 chr17 81195210 9626581 0.11856094712976295 0.3802515403041706 chr18 78077248 24760903 0.3171333984517487 0.6141701712044428 chr19 59128983 3507985 0.059327673537019905 0.25964371741886033 chr20 63025520 11550361 0.18326482669242555 0.4749292530882111 chr21 48129895 10328622 0.21459888911039593 0.5293338272235573 chr22 51304566 2995822 0.058392892359717063 0.2596861698619587 chrMT 16571 2777 0.16758192022207472 0.4207536972384969 chrX 155270560 20375182 0.13122372972700042 0.3782610788224018 chrY 59373566 3093782 0.052107060573050305 0.24898038251642338