BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081980.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 = 2,222,562 number of mapped reads = 2,063,076 (92.82%) number of supplementary alignments = 12,386 (0.56%) number of secondary alignments = 0 number of mapped bases = 139,972,401 bp number of sequenced bases = 139,920,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,228 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8692 >>>>>>> ACTG content number of A's = 39,462,395 bp (28.2%) number of C's = 25,557,420 bp (18.27%) number of T's = 44,753,354 bp (31.98%) number of G's = 30,129,294 bp (21.53%) number of N's = 18,129 bp (0.01%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,021,417 number of insertions = 9,689 mapped reads with insertion percentage = 0.47% number of deletions = 29,285 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.3853X There is a 3.88% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12963704 0.05201071896226088 0.6818149161634136 chr2 243199373 12632848 0.05194441023497211 0.48428178002126726 chr3 198022430 9130604 0.046108938265225816 0.24129524843341224 chr4 191154276 7545226 0.039471918483267414 0.23403772425591773 chr5 180915260 7115786 0.03933214920620848 0.2246063268737571 chr6 171115067 13081126 0.07644637161028023 0.3946231415360605 chr7 159138663 7705217 0.0484182589871325 0.5382487521974356 chr8 146364022 7744258 0.05291094009428082 0.5158348103654885 chr9 141213431 6560360 0.046457054074410246 0.3734043007590128 chr10 135534747 5716247 0.04217550942858955 0.37851808169192475 chr11 135006516 6535762 0.04841071522799685 0.28741237545350173 chr12 133851895 6257118 0.046746577625964875 0.2504516189364725 chr13 115169878 3862627 0.033538517771113725 0.2040006533344211 chr14 107349540 3478593 0.03240435869590126 0.21514746383124975 chr15 102531392 3005627 0.029314212373123736 0.19346797045531733 chr16 90354753 2711202 0.030006191262567008 0.21128214792858135 chr17 81195210 3752539 0.04621626078681242 0.2723164221561036 chr18 78077248 3341045 0.04279153127938116 0.5557317487573469 chr19 59128983 3078009 0.052055842056339785 0.521778469246816 chr20 63025520 3857321 0.061202525580114214 0.2860456622467224 chr21 48129895 1572636 0.03267482715264598 0.21759748289711375 chr22 51304566 1164979 0.022707121233614957 0.16707063384768456 chrMT 16571 47779 2.8832900850884076 2.277337946853281 chrX 155270560 6839955 0.04405184730447292 0.2665565064777331 chrY 59373566 271833 0.0045783505743953465 0.10926269170165788