BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472716.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,551,674 number of mapped reads = 12,447,878 (99.17%) number of supplementary alignments = 36,944 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,241,173 number of mapped paired reads (second in pair) = 6,206,705 number of mapped paired reads (both in pair) = 12,387,576 number of mapped paired reads (singletons) = 60,302 number of mapped bases = 1,223,910,468 bp number of sequenced bases = 1,223,753,778 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,210,157 duplication rate = 46.7% >>>>>>> Insert size mean insert size = 25,510.2681 std insert size = 1,628,201.4934 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.2431 >>>>>>> ACTG content number of A's = 330,559,558 bp (27.01%) number of C's = 283,147,083 bp (23.14%) number of T's = 329,198,843 bp (26.9%) number of G's = 280,610,193 bp (22.93%) number of N's = 238,101 bp (0.02%) GC percentage = 46.07% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 7,023,456 number of insertions = 64,698 mapped reads with insertion percentage = 0.51% number of deletions = 61,976 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.3954X std coverageData = 11.9701X There is a 3.58% of reference with a coverageData >= 1X There is a 1.58% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 132963621 0.5334535194598372 15.468547434688258 chr2 243199373 85158931 0.35016098088377884 11.34146014601685 chr3 198022430 142035454 0.7172695234575195 14.683312246364581 chr4 191154276 55640103 0.2910743309765145 9.973679676451296 chr5 180915260 62415849 0.3450004659640099 10.60280692023659 chr6 171115067 71368141 0.4170768959813457 10.593854492195344 chr7 159138663 45597938 0.2865296034314427 8.26879750993071 chr8 146364022 51562790 0.35229142582594514 10.839005605520455 chr9 141213431 72466947 0.513173191011838 15.792037005618942 chr10 135534747 30010922 0.2214260377082491 7.662743739629789 chr11 135006516 67861686 0.5026548940793346 15.254714065733138 chr12 133851895 53243353 0.3977781039259848 12.182118265384103 chr13 115169878 26089523 0.22653078611405666 7.713723663120655 chr14 107349540 30514825 0.28425669080649996 9.046715590585023 chr15 102531392 31157972 0.30388714511941867 9.40917185181039 chr16 90354753 38818499 0.4296232097496852 10.940499260917818 chr17 81195210 48477446 0.5970481017291537 14.54021122007522 chr18 78077248 20234751 0.25916321999463915 8.696673025243516 chr19 59128983 33530869 0.5670800899788857 12.08332670183251 chr20 63025520 24493264 0.38862454447024 10.933061553997215 chr21 48129895 4470877 0.0928918918273144 3.037632888712045 chr22 51304566 8810652 0.1717323171586716 4.437606575789411 chrMT 16571 2173 0.13113270170780278 0.42976102294323426 chrX 155270560 85013809 0.5475204636345744 18.356181719280688 chrY 59373566 1970073 0.03318097821512018 2.0472643531762773