BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081948.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 = 3,143,042 number of mapped reads = 2,887,293 (91.86%) number of supplementary alignments = 16,777 (0.53%) number of secondary alignments = 0 number of mapped bases = 195,897,706 bp number of sequenced bases = 195,818,291 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,818 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6655 >>>>>>> ACTG content number of A's = 55,219,107 bp (28.2%) number of C's = 35,828,475 bp (18.3%) number of T's = 62,393,192 bp (31.86%) number of G's = 42,352,668 bp (21.63%) number of N's = 24,849 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,502,702 number of insertions = 13,737 mapped reads with insertion percentage = 0.47% number of deletions = 44,956 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.5575X There is a 5.32% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16595714 0.06658243792299318 1.0105227812257316 chr2 243199373 17040325 0.0700673064646429 0.7458721858205565 chr3 198022430 12319201 0.062211139414863253 0.28459492445339685 chr4 191154276 9526977 0.04983920422475927 0.2965963467992531 chr5 180915260 11301727 0.06246972753984379 0.2880001630324126 chr6 171115067 16823603 0.0983174848068756 0.4945604905054674 chr7 159138663 12961006 0.08144473351519863 0.7974533885616226 chr8 146364022 10937263 0.07472644472696986 0.6864642568853984 chr9 141213431 11943522 0.08457780478402228 0.6065570817138131 chr10 135534747 7656672 0.05649231779655737 0.5491877935006251 chr11 135006516 8841554 0.0654898316167199 0.41959230123668784 chr12 133851895 8089950 0.06043956269726327 0.3006480572783651 chr13 115169878 5476631 0.04755263351064764 0.24635586921266503 chr14 107349540 4953515 0.04614379344336268 0.28110599878445797 chr15 102531392 4619014 0.04504975412798453 0.24407276613296036 chr16 90354753 3879877 0.04294048593105002 0.29973864289649915 chr17 81195210 6201267 0.07637478861129862 0.36785846711485476 chr18 78077248 6180054 0.07915307158367058 0.9757729499273818 chr19 59128983 2810750 0.04753590975850202 0.761714746045254 chr20 63025520 4821534 0.0765012966176241 0.3252432388213539 chr21 48129895 2114044 0.0439237193432481 0.28435041269635164 chr22 51304566 1633969 0.031848412868359516 0.1992401409877989 chrMT 16571 27133 1.6373785528936093 1.7348881599180026 chrX 155270560 8710722 0.05610028069712636 0.34597932325999814 chrY 59373566 431682 0.0072706092809045695 0.2019770659927797