BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234129.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,892,015 number of mapped reads = 3,461,314 (88.93%) number of supplementary alignments = 36,694 (0.94%) number of secondary alignments = 0 number of mapped bases = 239,528,179 bp number of sequenced bases = 239,453,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,209,228 duplication rate = 13.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4069 >>>>>>> ACTG content number of A's = 54,584,447 bp (22.8%) number of C's = 39,889,463 bp (16.66%) number of T's = 58,062,426 bp (24.25%) number of G's = 86,867,584 bp (36.28%) number of N's = 49,864 bp (0.02%) GC percentage = 52.94% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,341,284 number of insertions = 14,287 mapped reads with insertion percentage = 0.41% number of deletions = 45,434 mapped reads with deletion percentage = 1.3% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.0774X std coverageData = 85.4043X There is a 1.34% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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% 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 10191532 0.04088869251001786 0.8370893066110261 chr2 243199373 48794384 0.20063531989451305 304.6613855089589 chr3 198022430 10679535 0.053930936005582804 0.7295348051625494 chr4 191154276 8304441 0.0434436580429935 0.6654399098809236 chr5 180915260 4705381 0.02600875680691612 0.5123598879863613 chr6 171115067 8406452 0.049127479814504 2.9115067340978618 chr7 159138663 5072328 0.03187363714372792 0.6766021684036831 chr8 146364022 33764933 0.23069148099797368 1.6560392875573617 chr9 141213431 7421797 0.05255730242826548 0.749919154565329 chr10 135534747 2554586 0.018848199864201613 0.41588010769221634 chr11 135006516 8919064 0.06606395205398827 0.9161635068487863 chr12 133851895 4099165 0.030624631799198658 3.172603697069682 chr13 115169878 7540224 0.065470452265305 0.8481652450877989 chr14 107349540 9231265 0.0859925901871587 1.0167389641060738 chr15 102531392 2238268 0.021830075222230474 3.718605597573359 chr16 90354753 8473937 0.09378518250168864 0.9592616481636393 chr17 81195210 4314613 0.05313876274228492 0.7224129337789531 chr18 78077248 6531810 0.08365830209589355 0.9607464347841002 chr19 59128983 27117154 0.4586101878329279 2.3250157695533455 chr20 63025520 5071890 0.08047359228452221 0.923862951750583 chr21 48129895 3100227 0.06441374950018071 0.8313489432690878 chr22 51304566 1762721 0.034357975077695814 0.5689815134175981 chrMT 16571 199072 12.013276205419105 12.965549372201838 chrX 155270560 10642206 0.06853975409118122 0.8359855992276907 chrY 59373566 391194 0.006588689653574118 0.2267013849762618