BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089592.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 10,328,769 number of mapped reads = 6,848,098 (66.3%) number of supplementary alignments = 257 (0%) number of secondary alignments = 0 number of mapped bases = 322,001,855 bp number of sequenced bases = 321,938,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 360,115 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4633 >>>>>>> ACTG content number of A's = 93,793,547 bp (29.13%) number of C's = 66,011,019 bp (20.5%) number of T's = 92,363,202 bp (28.69%) number of G's = 69,363,507 bp (21.55%) number of N's = 407,701 bp (0.13%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 3,090,661 number of insertions = 15,039 mapped reads with insertion percentage = 0.22% number of deletions = 42,252 mapped reads with deletion percentage = 0.62% homopolymer indels = 43.62% >>>>>>> Coverage mean coverageData = 0.104X std coverageData = 0.5796X There is a 7.83% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 23683292 0.09501798593312231 0.8635172243920769 chr2 243199373 25662099 0.10551877121821363 0.6556674164291804 chr3 198022430 23162315 0.11696813840735112 0.43647832774949646 chr4 191154276 21595850 0.11297602361769819 0.45455678282723466 chr5 180915260 19585132 0.10825583203981798 0.4245125241891657 chr6 171115067 19812996 0.11578755949059705 0.5120390001963013 chr7 159138663 17819202 0.11197280198338729 0.7413113061261905 chr8 146364022 16352456 0.11172456028845668 0.7032557317742628 chr9 141213431 13734042 0.09725733524596537 0.5766081558389663 chr10 135534747 15807750 0.11663245293105538 0.6452715609699524 chr11 135006516 15246154 0.11292902336654626 0.5624433127050342 chr12 133851895 13216382 0.09873884863565062 0.4187176864239659 chr13 115169878 10607055 0.09209921191372626 0.3867664332375442 chr14 107349540 9986541 0.09302826076385609 0.4468300444151636 chr15 102531392 9168724 0.08942357868310225 0.38221672935323225 chr16 90354753 8729576 0.09661446365749016 0.4381822763979646 chr17 81195210 8351267 0.10285418314701077 0.46699437445306236 chr18 78077248 7784151 0.09969807081315162 0.8999958927718279 chr19 59128983 5949428 0.10061779685945216 0.7475801567029051 chr20 63025520 6585300 0.10448624620629865 0.44952052840472045 chr21 48129895 4341141 0.09019635301510631 0.44445057130813403 chr22 51304566 3729491 0.07269315951332675 0.3465824687248213 chrMT 16571 82372 4.970852694466236 4.19201224369403 chrX 155270560 20024425 0.12896472454275942 0.5523543683373157 chrY 59373566 984714 0.016585057397428344 0.22758099976081547