BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085133.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 = 2,324,918 number of mapped reads = 2,051,334 (88.23%) number of supplementary alignments = 23,238 (1%) number of secondary alignments = 0 number of mapped bases = 137,821,294 bp number of sequenced bases = 137,768,755 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,055 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7737 >>>>>>> ACTG content number of A's = 38,678,936 bp (28.08%) number of C's = 25,810,067 bp (18.73%) number of T's = 43,123,772 bp (31.3%) number of G's = 30,125,860 bp (21.87%) number of N's = 30,120 bp (0.02%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,237,332 number of insertions = 10,860 mapped reads with insertion percentage = 0.53% number of deletions = 32,917 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.3963X There is a 3.67% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.11% 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 10575129 0.04242769369068092 0.6097316227600332 chr2 243199373 10944703 0.04500300664837652 0.4378718616095968 chr3 198022430 9516520 0.04805778820106389 0.25580433572279854 chr4 191154276 9669543 0.05058502065629963 0.2704108654483348 chr5 180915260 9071602 0.05014282377285365 0.2627361641207685 chr6 171115067 8857421 0.05176295200235056 0.32651203510876103 chr7 159138663 7138200 0.04485522163774871 0.32609528106731267 chr8 146364022 7151209 0.048859063192455865 0.7751017876287114 chr9 141213431 5808404 0.04113209316470754 0.3726181521890779 chr10 135534747 6562790 0.04842145756172769 0.32071790002284056 chr11 135006516 6276911 0.04649339295593703 0.4330669239700929 chr12 133851895 6257240 0.046747489081122084 0.25650735128243407 chr13 115169878 4562958 0.03961936991892967 0.23341197452046833 chr14 107349540 4375968 0.040763733128246285 0.2561549626777692 chr15 102531392 3901928 0.03805593510327061 0.23443248021435542 chr16 90354753 3836461 0.042459979941509 0.263895030364763 chr17 81195210 2880019 0.03547030668434751 0.2629002980195991 chr18 78077248 3546885 0.04542789469218997 0.7283931662282668 chr19 59128983 2112036 0.035719132865857005 0.43931737327640735 chr20 63025520 2743439 0.04352901808664173 0.2507525107899216 chr21 48129895 1816565 0.037742966195957836 0.24105094713793948 chr22 51304566 1095761 0.021357962564189707 0.16755819557134574 chrMT 16571 334686 20.19709130408545 10.971938660940594 chrX 155270560 8429691 0.05429033681594244 0.3130212603520366 chrY 59373566 355225 0.005982881338136234 0.11629692614440369