BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085027.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 = 2,882,462 number of mapped reads = 2,612,471 (90.63%) number of supplementary alignments = 23,848 (0.83%) number of secondary alignments = 0 number of mapped bases = 173,357,740 bp number of sequenced bases = 173,297,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,595 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4133 >>>>>>> ACTG content number of A's = 48,844,944 bp (28.19%) number of C's = 31,738,639 bp (18.31%) number of T's = 54,458,154 bp (31.42%) number of G's = 38,231,878 bp (22.06%) number of N's = 24,329 bp (0.01%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,431,348 number of insertions = 13,450 mapped reads with insertion percentage = 0.51% number of deletions = 37,387 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.5394X There is a 4.89% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 13492478 0.0541321740578532 1.0972304037879068 chr2 243199373 14273762 0.05869160690640432 0.599584741505753 chr3 198022430 11867567 0.05993041798345773 0.2755899107170601 chr4 191154276 11941322 0.06246955208054043 0.28637187352194876 chr5 180915260 11050484 0.06108099449432845 0.27713411041564806 chr6 171115067 10564395 0.061738543456258003 0.4101255823344094 chr7 159138663 9614924 0.0604185294682286 0.49889597347464376 chr8 146364022 9108252 0.062230129204839696 0.8023221593374293 chr9 141213431 7348612 0.052039044359739405 0.48617285063243004 chr10 135534747 8104841 0.05979899014383374 0.5624321717726176 chr11 135006516 7872294 0.05831047443665608 0.5018090060476641 chr12 133851895 7995183 0.05973156375559718 0.2859881400578973 chr13 115169878 5831871 0.05063712058460286 0.24653325326777487 chr14 107349540 5260115 0.04899988393056924 0.29855491491051256 chr15 102531392 4500418 0.043893074230378144 0.24010338594649694 chr16 90354753 4603914 0.05095375558162391 0.3224433685229806 chr17 81195210 4210638 0.05185820690654042 0.3420953393776396 chr18 78077248 4782226 0.06124993032541311 1.0077163707346461 chr19 59128983 3002427 0.05077758567232587 0.7379346978292355 chr20 63025520 3288701 0.0521804659445888 0.27458777010276875 chr21 48129895 2253527 0.04682177262177696 0.26731768459443456 chr22 51304566 1602717 0.031239266306238706 0.1933123742908463 chrMT 16571 39196 2.3653370345784803 2.048141874378306 chrX 155270560 10352324 0.06667280648694769 0.36391541040729664 chrY 59373566 395552 0.006662089321028823 0.12428937101771938