BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089402.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 = 23,066,645 number of mapped reads = 20,819,912 (90.26%) number of supplementary alignments = 117,496 (0.51%) number of secondary alignments = 0 number of mapped bases = 1,388,990,342 bp number of sequenced bases = 1,388,500,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,019,457 duplication rate = 12.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4813 >>>>>>> ACTG content number of A's = 371,144,912 bp (26.73%) number of C's = 265,726,515 bp (19.14%) number of T's = 427,890,565 bp (30.82%) number of G's = 323,588,112 bp (23.3%) number of N's = 149,931 bp (0.01%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,027,221 number of insertions = 91,507 mapped reads with insertion percentage = 0.44% number of deletions = 276,809 mapped reads with deletion percentage = 1.31% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.4487X std coverageData = 2.9823X There is a 15.96% of reference with a coverageData >= 1X There is a 9.29% of reference with a coverageData >= 2X There is a 5.8% of reference with a coverageData >= 3X There is a 3.76% of reference with a coverageData >= 4X There is a 2.51% of reference with a coverageData >= 5X There is a 1.72% of reference with a coverageData >= 6X There is a 1.21% of reference with a coverageData >= 7X There is a 0.87% of reference with a coverageData >= 8X There is a 0.63% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 119460421 0.4792783284580061 5.724969612215723 chr2 243199373 148659629 0.6112664977964396 3.4985577015559577 chr3 198022430 87464501 0.44168986816291467 1.5249796161519549 chr4 191154276 67808260 0.3547305423604544 2.136676689160496 chr5 180915260 67411039 0.3726111274416542 1.3996265913221493 chr6 171115067 84685159 0.4949018253313719 2.139602201828839 chr7 159138663 75550799 0.47474823261522564 3.5729029612499565 chr8 146364022 77905667 0.5322733410537188 2.941016135362584 chr9 141213431 78965075 0.5591895504613864 3.03163324374784 chr10 135534747 52587071 0.3879969687773129 4.2648526556426 chr11 135006516 64869276 0.480489963906631 3.1281912623944765 chr12 133851895 75023929 0.560499565583289 1.7955176300214024 chr13 115169878 33508164 0.29094555435753783 1.1907316484307013 chr14 107349540 24230983 0.22572041761892972 1.3855677180114054 chr15 102531392 35058061 0.3419251442524061 1.3001505017446338 chr16 90354753 34482236 0.38163167797049924 1.8162884588091681 chr17 81195210 33546932 0.41316392925149154 1.8709433148682386 chr18 78077248 42942693 0.5500026460973625 4.503943912837796 chr19 59128983 28911814 0.48896180067903416 4.017475695624247 chr20 63025520 31252228 0.4958662459270467 1.8544106814178094 chr21 48129895 13489244 0.28026747201505425 1.9597239391945012 chr22 51304566 20029117 0.39039638304317786 1.472954326204354 chrMT 16571 187262 11.300585359966206 8.079298246282125 chrX 155270560 87354047 0.5625924644053579 2.1246599607016394 chrY 59373566 3606735 0.06074647764966652 1.7658849349940413