BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082952.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 = 1,641,430 number of mapped reads = 1,502,077 (91.51%) number of supplementary alignments = 16,409 (1%) number of secondary alignments = 0 number of mapped bases = 101,197,910 bp number of sequenced bases = 101,159,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,841 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0751 >>>>>>> ACTG content number of A's = 28,301,751 bp (27.98%) number of C's = 18,390,074 bp (18.18%) number of T's = 32,549,805 bp (32.18%) number of G's = 21,912,224 bp (21.66%) number of N's = 5,350 bp (0.01%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 709,182 number of insertions = 8,633 mapped reads with insertion percentage = 0.57% number of deletions = 23,957 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.14% >>>>>>> Coverage mean coverageData = 0.0327X std coverageData = 0.2724X There is a 2.8% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 9537820 0.03826598289598645 0.4102669646297 chr2 243199373 10345256 0.04253816887924296 0.36860987944183554 chr3 198022430 7507055 0.03791012462578103 0.21977997234194868 chr4 191154276 7116770 0.03723050380520915 0.2247047801482776 chr5 180915260 5883654 0.03252160154980846 0.2098287813941815 chr6 171115067 6247330 0.03650952607230081 0.24763358888155507 chr7 159138663 6191843 0.03890847694252653 0.28132387944400816 chr8 146364022 8812615 0.0602102544025471 0.40544116963861626 chr9 141213431 2908205 0.020594393744317423 0.2453623529199812 chr10 135534747 3465000 0.025565399845399055 0.20769547841799105 chr11 135006516 4373140 0.03239206617256903 0.23864486534477872 chr12 133851895 2985761 0.02230645296430058 0.2298397434232837 chr13 115169878 2176286 0.01889631245419918 0.1557092118214767 chr14 107349540 1979752 0.0184421097659105 0.16451647368678896 chr15 102531392 1905908 0.01858853140314334 0.1594537418775515 chr16 90354753 3189215 0.03529659363907508 0.22208885975354387 chr17 81195210 2469865 0.030418851062765893 0.21350027314084166 chr18 78077248 3267346 0.04184760712877585 0.45142290224755566 chr19 59128983 1631387 0.027590310491218833 0.2828482576423878 chr20 63025520 1913713 0.030364096956280565 0.20216731060637227 chr21 48129895 1529406 0.031776632797557526 0.20397202410869836 chr22 51304566 1209078 0.02356667435798989 0.17048797941975208 chrMT 16571 125219 7.556514392613602 5.1751386103208485 chrX 155270560 4256741 0.027414990968023818 0.19738490072360879 chrY 59373566 169545 0.0028555637032143225 0.06641532876820702