BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153324.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 130,158,636 number of mapped reads = 126,236,035 (96.99%) number of supplementary alignments = 795,850 (0.61%) number of secondary alignments = 0 number of mapped bases = 12,415,400,733 bp number of sequenced bases = 12,413,326,146 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,815,513 duplication rate = 33.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2852 >>>>>>> ACTG content number of A's = 3,104,438,919 bp (25.01%) number of C's = 3,102,416,273 bp (24.99%) number of T's = 3,132,183,961 bp (25.23%) number of G's = 3,071,748,135 bp (24.75%) number of N's = 2,538,858 bp (0.02%) GC percentage = 49.74% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 49,305,350 number of insertions = 726,371 mapped reads with insertion percentage = 0.57% number of deletions = 933,457 mapped reads with deletion percentage = 0.73% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 4.0105X std coverageData = 31.9809X There is a 50.55% of reference with a coverageData >= 1X There is a 32.35% of reference with a coverageData >= 2X There is a 21.06% of reference with a coverageData >= 3X There is a 14.87% of reference with a coverageData >= 4X There is a 11.13% of reference with a coverageData >= 5X There is a 8.84% of reference with a coverageData >= 6X There is a 7.34% of reference with a coverageData >= 7X There is a 6.32% of reference with a coverageData >= 8X There is a 5.59% of reference with a coverageData >= 9X There is a 5.05% of reference with a coverageData >= 10X There is a 4.63% of reference with a coverageData >= 11X There is a 4.3% of reference with a coverageData >= 12X There is a 4.03% of reference with a coverageData >= 13X There is a 3.8% of reference with a coverageData >= 14X There is a 3.6% of reference with a coverageData >= 15X There is a 3.43% of reference with a coverageData >= 16X There is a 3.28% of reference with a coverageData >= 17X There is a 3.15% of reference with a coverageData >= 18X There is a 3.02% of reference with a coverageData >= 19X There is a 2.91% of reference with a coverageData >= 20X There is a 2.81% of reference with a coverageData >= 21X There is a 2.72% of reference with a coverageData >= 22X There is a 2.63% of reference with a coverageData >= 23X There is a 2.55% of reference with a coverageData >= 24X There is a 2.47% of reference with a coverageData >= 25X There is a 2.4% of reference with a coverageData >= 26X There is a 2.34% of reference with a coverageData >= 27X There is a 2.27% of reference with a coverageData >= 28X There is a 2.21% of reference with a coverageData >= 29X There is a 2.16% of reference with a coverageData >= 30X There is a 2.1% of reference with a coverageData >= 31X There is a 2.05% of reference with a coverageData >= 32X There is a 2% of reference with a coverageData >= 33X There is a 1.95% of reference with a coverageData >= 34X There is a 1.91% of reference with a coverageData >= 35X There is a 1.87% of reference with a coverageData >= 36X There is a 1.82% of reference with a coverageData >= 37X There is a 1.78% of reference with a coverageData >= 38X There is a 1.75% of reference with a coverageData >= 39X There is a 1.71% of reference with a coverageData >= 40X There is a 1.67% of reference with a coverageData >= 41X There is a 1.64% of reference with a coverageData >= 42X There is a 1.6% of reference with a coverageData >= 43X There is a 1.57% of reference with a coverageData >= 44X There is a 1.54% of reference with a coverageData >= 45X There is a 1.51% of reference with a coverageData >= 46X There is a 1.48% of reference with a coverageData >= 47X There is a 1.46% of reference with a coverageData >= 48X There is a 1.43% of reference with a coverageData >= 49X There is a 1.4% of reference with a coverageData >= 50X There is a 1.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1186360259 4.759708337898183 31.634400946331034 chr2 243199373 701369554 2.883928298614487 16.555047619980826 chr3 198022430 585286658 2.9556583968795858 16.772582618793425 chr4 191154276 387494467 2.0271294742054318 21.248384579358007 chr5 180915260 712408113 3.9378000120056207 59.80092434019179 chr6 171115067 349598703 2.0430620700396886 13.43755217332848 chr7 159138663 656433872 4.124917600947797 34.00847593172135 chr8 146364022 745840113 5.095788587990565 60.57889356788743 chr9 141213431 301571104 2.135569554995091 12.893442617114314 chr10 135534747 583822170 4.307546093696549 23.22291379190977 chr11 135006516 573308050 4.2465213308667265 22.54482558423839 chr12 133851895 517888365 3.8691149273605725 20.249588971133093 chr13 115169878 102408338 0.8891937699195965 6.390509764338559 chr14 107349540 321774686 2.9974482051809446 17.629750665892043 chr15 102531392 716311780 6.986267971471605 41.27882045578053 chr16 90354753 714173009 7.9041000643319785 47.17511133906522 chr17 81195210 730862763 9.00130393159892 48.61557335886337 chr18 78077248 120722565 1.5461939052974818 11.52993960746924 chr19 59128983 902023919 15.255190825791813 58.00697569935473 chr20 63025520 379906867 6.027825982237037 29.519696794125633 chr21 48129895 137785805 2.862790475649282 27.939517496612286 chr22 51304566 357578036 6.969711740666513 40.128358567436834 chrMT 16571 166424 10.043087321223824 5.047562049230364 chrX 155270560 613329883 3.9500719453835935 21.755316398429603 chrY 59373566 16975230 0.2859055155959472 11.191446191530249