BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080956.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 = 4,750,328 number of mapped reads = 4,361,206 (91.81%) number of supplementary alignments = 66,609 (1.4%) number of secondary alignments = 0 number of mapped bases = 303,020,270 bp number of sequenced bases = 302,906,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,651 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4292 >>>>>>> ACTG content number of A's = 88,985,003 bp (29.38%) number of C's = 54,451,796 bp (17.98%) number of T's = 95,937,313 bp (31.67%) number of G's = 62,066,200 bp (20.49%) number of N's = 1,466,494 bp (0.48%) GC percentage = 38.47% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 3,521,219 number of insertions = 23,907 mapped reads with insertion percentage = 0.54% number of deletions = 68,534 mapped reads with deletion percentage = 1.55% homopolymer indels = 49.46% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 0.6725X There is a 6.58% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% 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% 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 24489994 0.09825449542209967 0.8493693558962339 chr2 243199373 20807544 0.08555755610439011 0.6122865465462083 chr3 198022430 27577616 0.13926511254305887 0.5167671721937043 chr4 191154276 19433066 0.10166168608229302 0.4717407276207779 chr5 180915260 17847531 0.09865132990992578 0.4325184839350152 chr6 171115067 26387848 0.15421113092279595 0.7435169883588605 chr7 159138663 14528178 0.09129257294313199 0.6194663862221078 chr8 146364022 23662620 0.16166964856978308 1.5426454917530632 chr9 141213431 15567822 0.11024321050594685 0.7864906847034093 chr10 135534747 13802727 0.10183902877687889 0.5806574256238151 chr11 135006516 13346768 0.09886017649696256 0.5085476273197184 chr12 133851895 15833272 0.11828948704835296 0.4970218730917342 chr13 115169878 8145216 0.07072349247430826 0.3636251786235063 chr14 107349540 8800587 0.0819806680121778 0.5226431609703236 chr15 102531392 7896765 0.07701802195370565 0.37891873463420794 chr16 90354753 6914605 0.0765272967986532 0.4782642288432313 chr17 81195210 6149843 0.07574145075799422 0.38746482059337645 chr18 78077248 5052315 0.06470918390976076 1.2433619360442758 chr19 59128983 5043008 0.08528825872076981 0.678901128667583 chr20 63025520 4128109 0.06549900738621435 0.37519824589317113 chr21 48129895 5649315 0.11737642477715773 0.5646827678196763 chr22 51304566 2382289 0.046434249146557444 0.2869618821662268 chrMT 16571 20264 1.2228592118761692 1.5917566410374373 chrX 155270560 8888673 0.05724635114344922 0.360471833822695 chrY 59373566 664295 0.011188396533231641 0.2278229498648582