BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708596.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,830,962 number of mapped reads = 3,746,984 (97.81%) number of supplementary alignments = 114 (0%) number of secondary alignments = 0 number of mapped bases = 186,869,426 bp number of sequenced bases = 186,853,180 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,172 duplication rate = 0.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.716 >>>>>>> ACTG content number of A's = 57,974,758 bp (31.03%) number of C's = 35,313,074 bp (18.9%) number of T's = 57,727,282 bp (30.89%) number of G's = 35,831,439 bp (19.18%) number of N's = 6,627 bp (0%) GC percentage = 38.08% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 272,774 number of insertions = 11,884 mapped reads with insertion percentage = 0.32% number of deletions = 9,593 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.2549X There is a 5.66% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 14332287 0.05750150969533593 0.25036344400775024 chr2 243199373 16473950 0.06773845588820658 0.26892445945413695 chr3 198022430 14060486 0.07100451196361947 0.2753365934111144 chr4 191154276 14936498 0.0781384456186583 0.28885431358529434 chr5 180915260 13289760 0.07345847995354289 0.2799562677713511 chr6 171115067 12047486 0.07040575801545285 0.2742072846720708 chr7 159138663 10437169 0.06558537569214089 0.26545698459700584 chr8 146364022 10227449 0.06987679663517309 0.2732812749636879 chr9 141213431 7877489 0.055784275930523916 0.24557229240025663 chr10 135534747 7556290 0.05575168115376347 0.24355058105737268 chr11 135006516 8775545 0.0650008996602801 0.2650283240976366 chr12 133851895 8578204 0.06408728094585438 0.2622879061444357 chr13 115169878 7222146 0.0627086363675752 0.25953892708123205 chr14 107349540 5840572 0.05440705195383231 0.24183648022912868 chr15 102531392 4988473 0.04865312859499654 0.2295331169861359 chr16 90354753 3413312 0.03777678413884879 0.2010637675277308 chr17 81195210 2996304 0.03690247244880578 0.19883984194640933 chr18 78077248 5398988 0.06914931222985728 0.2720357081635914 chr19 59128983 1468788 0.02484040694560906 0.16178976272991571 chr20 63025520 3073771 0.04877026004704126 0.22970880712654462 chr21 48129895 2239632 0.04653307471375119 0.22465262517522874 chr22 51304566 1065009 0.02075856172333667 0.14939726050782431 chrMT 16571 350 0.021121235894031743 0.1437884880243909 chrX 155270560 10331015 0.06653556862292505 0.26666348872191 chrY 59373566 238453 0.004016147522619746 0.06587516030085847