BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081023.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 = 2,302,150 number of mapped reads = 1,713,924 (74.45%) number of supplementary alignments = 6,254 (0.27%) number of secondary alignments = 0 number of mapped bases = 103,210,363 bp number of sequenced bases = 103,174,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,868 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2795 >>>>>>> ACTG content number of A's = 29,384,578 bp (28.48%) number of C's = 21,123,386 bp (20.47%) number of T's = 29,500,965 bp (28.59%) number of G's = 23,164,622 bp (22.45%) number of N's = 1,234 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 753,096 number of insertions = 6,877 mapped reads with insertion percentage = 0.4% number of deletions = 20,347 mapped reads with deletion percentage = 1.18% homopolymer indels = 44.8% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.2737X There is a 2.97% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8424968 0.03380119161267807 0.4347860759616203 chr2 243199373 8795908 0.03616747811270056 0.3049062906478155 chr3 198022430 6102321 0.030816312071314345 0.19154634791670155 chr4 191154276 6947526 0.03634512470963506 0.22122016885341075 chr5 180915260 6277308 0.03469750423485559 0.2036204190299789 chr6 171115067 6337394 0.03703586195597843 0.2682781777176402 chr7 159138663 5631217 0.03538559953843523 0.3681508309503924 chr8 146364022 4982484 0.03404172645651948 0.2628201016246909 chr9 141213431 4584961 0.03246830678591755 0.26058905234168067 chr10 135534747 4550441 0.03357398084787807 0.25638466972114 chr11 135006516 4883272 0.03617063934899261 0.2788139697377353 chr12 133851895 4669026 0.034882031367579815 0.20653792433043497 chr13 115169878 2982605 0.02589743995387405 0.17483555147168617 chr14 107349540 2944542 0.027429479436986873 0.19132674349904788 chr15 102531392 3100676 0.030241235776843838 0.19751354592245704 chr16 90354753 3203730 0.03545723820417062 0.22466150896417125 chr17 81195210 2903423 0.035758550288865563 0.22559018766224576 chr18 78077248 2869308 0.03674960469918202 0.46251284448021124 chr19 59128983 2170996 0.036716274994954674 0.34973453029935225 chr20 63025520 2261804 0.035887113664433076 0.21231403561663614 chr21 48129895 1423251 0.0295710389561415 0.20368179844191417 chr22 51304566 1269591 0.024746160020143237 0.1719819854995524 chrMT 16571 17319 1.0451390984249593 1.1571998490331596 chrX 155270560 5610907 0.03613632230089207 0.2269312138560419 chrY 59373566 265385 0.004469750056784529 0.1141201002921999