BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085111.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 = 1,085,656 number of mapped reads = 852,631 (78.54%) number of supplementary alignments = 6,528 (0.6%) number of secondary alignments = 0 number of mapped bases = 57,749,818 bp number of sequenced bases = 57,729,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,553 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0306 >>>>>>> ACTG content number of A's = 17,450,013 bp (30.23%) number of C's = 10,412,732 bp (18.04%) number of T's = 17,240,407 bp (29.86%) number of G's = 12,625,025 bp (21.87%) number of N's = 1,197 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 569,068 number of insertions = 4,367 mapped reads with insertion percentage = 0.51% number of deletions = 12,598 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.0187X std coverageData = 0.161X There is a 1.76% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 6445949 0.025861315707614626 0.23728253500322743 chr2 243199373 6091581 0.0250476838194809 0.1761710002946597 chr3 198022430 3290843 0.016618536597091553 0.13516433165954703 chr4 191154276 3864686 0.020217627776215687 0.14818418839840897 chr5 180915260 3084126 0.017047351340069378 0.13572045675377037 chr6 171115067 3693779 0.02158652107473388 0.16443499846897922 chr7 159138663 4681346 0.029416773471321673 0.18597805752488933 chr8 146364022 3985960 0.027233195327195914 0.24475156079668603 chr9 141213431 1691128 0.011975688063269279 0.12227289073838275 chr10 135534747 3202800 0.02363084058437059 0.1885002837857442 chr11 135006516 2632625 0.01949998472666312 0.16310399391301755 chr12 133851895 2302628 0.017202804637170062 0.13706567128962605 chr13 115169878 1038321 0.00901556047493599 0.09839464236355995 chr14 107349540 2019677 0.018814025658610182 0.14347557535215713 chr15 102531392 854160 0.008330716898879126 0.09432548714254847 chr16 90354753 1339006 0.014819430694476029 0.12862367423335472 chr17 81195210 506229 0.006234715077404197 0.08331392237365443 chr18 78077248 1589151 0.020353573425128918 0.18205078208879338 chr19 59128983 887024 0.015001509496620295 0.160114063036021 chr20 63025520 1260011 0.019992076225630505 0.14756226717255147 chr21 48129895 697895 0.0145002394042206 0.12635446300472064 chr22 51304566 452131 0.008812685405037829 0.09747168955663939 chrMT 16571 4688 0.282903868203488 0.5828453278678617 chrX 155270560 2043823 0.013162978223302601 0.1227285858921702 chrY 59373566 90251 0.001520053553798672 0.044649905834540926