BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230349.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 = 2,169,418 number of mapped reads = 1,754,860 (80.89%) number of supplementary alignments = 8,025 (0.37%) number of secondary alignments = 0 number of mapped bases = 111,333,796 bp number of sequenced bases = 111,285,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,888 duplication rate = 2.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1925 >>>>>>> ACTG content number of A's = 29,107,340 bp (26.16%) number of C's = 18,483,345 bp (16.61%) number of T's = 37,536,443 bp (33.73%) number of G's = 25,956,537 bp (23.32%) number of N's = 201,677 bp (0.18%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,024,629 number of insertions = 10,475 mapped reads with insertion percentage = 0.59% number of deletions = 29,600 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3946X There is a 3.21% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8626777 0.03461085459040842 0.6431332938581245 chr2 243199373 10564224 0.04343853304259958 0.4534654171792044 chr3 198022430 7824057 0.03951096348024817 0.218597225221844 chr4 191154276 7071871 0.03699562022876224 0.22675936868435265 chr5 180915260 6499419 0.03592521161564812 0.20788235565472316 chr6 171115067 6093151 0.03560850079905588 0.2919199583349985 chr7 159138663 5380346 0.033809169302873934 0.45769742498956684 chr8 146364022 5716746 0.03905841013305852 0.5892877112586394 chr9 141213431 5320395 0.037676267493281144 0.5054704164174846 chr10 135534747 4712118 0.03476686314248257 0.37341771539059054 chr11 135006516 5396645 0.03997321877412199 0.42918748607991447 chr12 133851895 4650063 0.03474035985818505 0.2152508411229863 chr13 115169878 4110103 0.035687308794405424 0.20287022395450297 chr14 107349540 3939817 0.036700827968149656 0.24732691601710685 chr15 102531392 3145210 0.030675580801633903 0.189934962200672 chr16 90354753 2567037 0.028410647085715567 0.24515318905861366 chr17 81195210 2331179 0.02871079463924042 0.21785701885854403 chr18 78077248 2985266 0.038234774873212744 0.8591743984662112 chr19 59128983 1645964 0.027836839338163485 0.4526374060254542 chr20 63025520 2132886 0.03384162478945037 0.23075894654140547 chr21 48129895 1577515 0.032776198659897345 0.22277315697951985 chr22 51304566 963056 0.0187713506825104 0.14747265961136416 chrMT 16571 51167 3.087743648542635 2.9229347106435086 chrX 155270560 7696712 0.049569680176332204 0.30785666750367796 chrY 59373566 332072 0.005592926656957071 0.12779060010349455