BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081212.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 9,229,522 number of mapped reads = 8,261,670 (89.51%) number of supplementary alignments = 44,774 (0.49%) number of secondary alignments = 0 number of mapped bases = 574,170,977 bp number of sequenced bases = 573,954,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 377,187 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7461 >>>>>>> ACTG content number of A's = 170,614,547 bp (29.73%) number of C's = 108,603,299 bp (18.92%) number of T's = 176,892,818 bp (30.82%) number of G's = 117,695,469 bp (20.51%) number of N's = 148,265 bp (0.03%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 6,234,374 number of insertions = 43,434 mapped reads with insertion percentage = 0.52% number of deletions = 136,841 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.74% >>>>>>> Coverage mean coverageData = 0.1855X std coverageData = 2.0392X There is a 13.53% of reference with a coverageData >= 1X There is a 3.29% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.23% 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 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 62066233 0.24901134749830775 4.890307781983599 chr2 243199373 37781247 0.15535092271804501 1.3449300719913426 chr3 198022430 38143803 0.19262364874524568 0.8297290463114277 chr4 191154276 25950440 0.1357565236992135 0.49030099183666126 chr5 180915260 34205589 0.18906967272965255 0.5696610955384782 chr6 171115067 41909967 0.2449227162445023 1.147038722126489 chr7 159138663 39753872 0.24980649736890148 3.1449596807926112 chr8 146364022 37854212 0.2586305806764452 2.798741736994552 chr9 141213431 15708715 0.11124094138042719 1.1434176167599541 chr10 135534747 19428744 0.14334880486403978 3.116432345379775 chr11 135006516 31434040 0.2328335026436798 1.7250120649137592 chr12 133851895 16626487 0.12421555182315498 0.4994891206960226 chr13 115169878 17571182 0.1525675142245093 0.4763307275192712 chr14 107349540 21759690 0.2026994247017733 0.65917441251793 chr15 102531392 10179767 0.0992843928228342 0.37911198921659195 chr16 90354753 18184464 0.20125630801071417 0.8207581481487162 chr17 81195210 8430532 0.10383041068555646 0.6963176088566115 chr18 78077248 14918116 0.19106867086298943 2.2015018037968446 chr19 59128983 12715783 0.21505161013846627 3.1749330363524964 chr20 63025520 14059474 0.2230758905281543 0.6217749234675707 chr21 48129895 9169402 0.1905136506115378 0.6637063063434361 chr22 51304566 3448462 0.06721549890900548 0.32204341473211073 chrMT 16571 13333 0.8045983947860721 1.030595502244241 chrX 155270560 41434593 0.2668541480110589 0.8740250053839096 chrY 59373566 1422830 0.02396403140077522 0.34009251149983705