BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505981.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 = 9,493,380 number of mapped reads = 6,997,821 (73.71%) number of supplementary alignments = 295 (0%) number of secondary alignments = 0 number of mapped bases = 327,298,938 bp number of sequenced bases = 327,234,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,035 duplication rate = 4.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3924 >>>>>>> ACTG content number of A's = 100,857,832 bp (30.82%) number of C's = 63,228,261 bp (19.32%) number of T's = 99,027,612 bp (30.26%) number of G's = 64,119,804 bp (19.59%) number of N's = 1,463 bp (0%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,525,036 number of insertions = 15,669 mapped reads with insertion percentage = 0.22% number of deletions = 47,327 mapped reads with deletion percentage = 0.67% homopolymer indels = 47.74% >>>>>>> Coverage mean coverageData = 0.1057X std coverageData = 0.9447X There is a 7.13% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 25900864 0.10391494270339251 1.9451401900994425 chr2 243199373 27667607 0.11376512471518584 0.7971216013742947 chr3 198022430 22463767 0.1134405178241677 0.48367138761725614 chr4 191154276 23133824 0.12102174476076068 0.4914229466017202 chr5 180915260 20464934 0.11311889334266219 0.481264994533059 chr6 171115067 19709515 0.11518281438068806 0.5861821625532707 chr7 159138663 18379329 0.11549254375726406 1.1566941780625313 chr8 146364022 17753484 0.12129677606153785 1.7434159631680406 chr9 141213431 13630762 0.09652596005545676 0.6858447870836306 chr10 135534747 16123386 0.11896127271333601 0.9887108312300669 chr11 135006516 14749609 0.10925108977702973 0.7905672418236768 chr12 133851895 14535461 0.10859361385955724 0.5058704324017256 chr13 115169878 10701670 0.09292073748658482 0.41238752666726874 chr14 107349540 9935070 0.09254878968275039 0.4729809339030529 chr15 102531392 9111535 0.088865808044428 0.40453470576127076 chr16 90354753 7581124 0.0839039867664737 0.48269030013628955 chr17 81195210 7514324 0.09254639528612586 0.5613545871746158 chr18 78077248 9314556 0.11929923554682666 1.5707696221432486 chr19 59128983 5134430 0.08683440403498907 1.2769292541689563 chr20 63025520 6114972 0.09702374530190311 0.4379457831970405 chr21 48129895 4415251 0.09173614444826858 0.4743179540282342 chr22 51304566 3156077 0.06151649348325059 0.32957066463774687 chrMT 16571 28609 1.7264498219781546 1.9291759604970122 chrX 155270560 18968151 0.12216192818522713 0.6612318513378633 chrY 59373566 810627 0.013652995004544616 0.2227960083950544