BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548955.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 12,973,641 number of mapped reads = 11,368,790 (87.63%) number of secondary alignments = 0 number of mapped bases = 450,175,489 bp number of sequenced bases = 450,129,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 559,328 duplication rate = 3.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3815 >>>>>>> ACTG content number of A's = 128,344,456 bp (28.51%) number of C's = 95,496,460 bp (21.22%) number of T's = 130,530,585 bp (29%) number of G's = 95,756,882 bp (21.27%) number of N's = 672 bp (0%) GC percentage = 42.49% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 1,215,217 number of insertions = 13,791 mapped reads with insertion percentage = 0.12% number of deletions = 35,128 mapped reads with deletion percentage = 0.31% homopolymer indels = 41.05% >>>>>>> Coverage mean coverageData = 0.1454X std coverageData = 1.2693X There is a 11.18% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 36790892 0.1476060194048624 2.1849381567523483 chr2 243199373 38475126 0.15820405096192414 0.913446739546346 chr3 198022430 31021851 0.15665826845979014 0.4871916178925429 chr4 191154276 30118397 0.15756067627804465 0.5346616289384479 chr5 180915260 28343133 0.1566652420586301 0.5008832995032774 chr6 171115067 26751890 0.15633859992001756 0.5559249375525818 chr7 159138663 25724418 0.16164782030373095 1.7015387487052867 chr8 146364022 23515921 0.160667359906248 3.5812763206512988 chr9 141213431 19148879 0.13560239181498251 0.9059053286011219 chr10 135534747 21476666 0.15845874563812037 0.8493858408954066 chr11 135006516 20659901 0.153028917507952 0.7435598406587194 chr12 133851895 20900205 0.15614425929494685 0.5248649033962905 chr13 115169878 14728217 0.12788254407979838 0.4295861294474664 chr14 107349540 14057001 0.13094607578197354 0.6135318031490383 chr15 102531392 12907284 0.1258861676236679 0.4362775389269558 chr16 90354753 12559973 0.13900733036146976 0.5506261770906282 chr17 81195210 11815927 0.1455249269014761 0.5146136553054005 chr18 78077248 12108893 0.15508862453758615 1.754476120587895 chr19 59128983 9211179 0.15578111668181405 1.971097729958765 chr20 63025520 9286860 0.14735078742706129 0.508942605552127 chr21 48129895 5892311 0.1224251787792182 0.6085724353038814 chr22 51304566 5142538 0.10023548391384891 0.6667106577913707 chrMT 16571 28182 1.7006819141874359 2.2853653095609547 chrX 155270560 15562504 0.10022829826851916 0.586622737568229 chrY 59373566 3947341 0.06648313830434237 0.5782316119320307