BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083096.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 = 4,037,566 number of mapped reads = 3,332,663 (82.54%) number of supplementary alignments = 28,083 (0.7%) number of secondary alignments = 0 number of mapped bases = 220,592,735 bp number of sequenced bases = 220,502,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,076 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6252 >>>>>>> ACTG content number of A's = 60,639,353 bp (27.5%) number of C's = 41,255,416 bp (18.71%) number of T's = 68,695,245 bp (31.15%) number of G's = 49,891,675 bp (22.63%) number of N's = 20,859 bp (0.01%) GC percentage = 41.34% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 2,061,341 number of insertions = 19,396 mapped reads with insertion percentage = 0.58% number of deletions = 52,360 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0713X std coverageData = 0.7398X There is a 5.84% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21286121 0.0854004732850796 1.4431128026990374 chr2 243199373 22398753 0.09210037313706397 1.0850204818630522 chr3 198022430 15567044 0.07861252889382278 0.33015304669095447 chr4 191154276 11500465 0.06016326310168442 0.3077892065410289 chr5 180915260 12162499 0.06722760147485624 0.30865544100509423 chr6 171115067 15045978 0.08792900744386233 0.6426771932518571 chr7 159138663 10919517 0.06861636760137918 0.7545863384443872 chr8 146364022 19166320 0.13094966739845398 0.8088819946550231 chr9 141213431 6356094 0.04501054860709389 0.7376678706224337 chr10 135534747 7279281 0.0537078583988503 0.5826248754638753 chr11 135006516 9009173 0.06673139391286861 0.5620881482843226 chr12 133851895 7136737 0.05331816183850068 0.3024179491768654 chr13 115169878 4975084 0.043197788227230735 0.23636682585935062 chr14 107349540 4670793 0.04351013520877686 0.35555871355011337 chr15 102531392 4609121 0.04495326660541193 0.2525861021145741 chr16 90354753 9440841 0.10448637937176365 0.4914449085719529 chr17 81195210 6057142 0.07459974547759653 0.5019739974237414 chr18 78077248 7585816 0.09715783015302998 1.6559717314870828 chr19 59128983 4398390 0.0743863631140079 1.0074618487009062 chr20 63025520 4461526 0.07078919777258481 0.3686698810742073 chr21 48129895 3976679 0.08262388687945403 0.35773699227267547 chr22 51304566 2932231 0.057153412037439316 0.2776738057472132 chrMT 16571 136011 8.207772614809004 6.183297525399069 chrX 155270560 9088549 0.058533626722283995 0.443569372399516 chrY 59373566 432570 0.007285565431592908 0.1546729513216625