BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124798.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 = 763,555 number of mapped reads = 762,283 (99.83%) number of supplementary alignments = 295,337 (38.68%) number of secondary alignments = 0 number of mapped bases = 113,282,464 bp number of sequenced bases = 113,253,432 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,052,079 duplication rate = 7.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8275 >>>>>>> ACTG content number of A's = 38,735,661 bp (34.2%) number of C's = 24,502,611 bp (21.64%) number of T's = 31,523,799 bp (27.83%) number of G's = 18,491,361 bp (16.33%) number of N's = 0 bp (0%) GC percentage = 37.96% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,096,880 number of insertions = 5,483 mapped reads with insertion percentage = 0.72% number of deletions = 28,175 mapped reads with deletion percentage = 3.67% homopolymer indels = 57.04% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 109.2113X There is a 0.02% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 265653 0.0010658067728545398 0.7785677706448989 chr2 243199373 67489 2.775048272842381E-4 0.13944881680544627 chr3 198022430 72485 3.66044392041851E-4 0.18971848026260976 chr4 191154276 34566 1.808277623881142E-4 0.016532946027874106 chr5 180915260 30583 1.690459942406185E-4 0.013033155194194368 chr6 171115067 32119 1.8770410205899636E-4 0.013906059730720899 chr7 159138663 66745 4.194141055464315E-4 0.24588672071590958 chr8 146364022 1164587 0.007956784625664359 5.310975464602844 chr9 141213431 19097 1.3523501174615607E-4 0.011657163871412659 chr10 135534747 111232544 0.8206939287679491 521.9095371510012 chr11 135006516 20620 1.527333688101395E-4 0.012476003386481424 chr12 133851895 29570 2.2091581146460422E-4 0.015952627617123738 chr13 115169878 10414 9.04229489589283E-5 0.00950684214798109 chr14 107349540 58544 5.453586480202896E-4 0.4845663683744088 chr15 102531392 41241 4.022280317817201E-4 0.1571379165678469 chr16 90354753 24260 2.684972200632323E-4 0.017505491604227985 chr17 81195210 13779 1.6970212898026867E-4 0.013949501982740477 chr18 78077248 8431 1.079828018528522E-4 0.010388451343567397 chr19 59128983 15796 2.6714479428810743E-4 0.031517457660578854 chr20 63025520 17509 2.778081005916334E-4 0.018484413433043984 chr21 48129895 7535 1.5655550464009946E-4 0.012511234751776755 chr22 51304566 4921 9.591738871740967E-5 0.009793272618075702 chrMT 16571 991 0.05980327077424416 0.2776809138560007 chrX 155270560 31383 2.021181607125008E-4 0.057131627743920735 chrY 59373566 11602 1.954068246465102E-4 0.015606256191433954