BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472784.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,647,230 number of mapped reads = 10,546,033 (99.05%) number of supplementary alignments = 43,126 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,289,722 number of mapped paired reads (second in pair) = 5,256,311 number of mapped paired reads (both in pair) = 10,489,652 number of mapped paired reads (singletons) = 56,381 number of mapped bases = 1,037,288,800 bp number of sequenced bases = 1,037,154,428 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,162,597 duplication rate = 44.65% >>>>>>> Insert size mean insert size = 27,246.8624 std insert size = 1,619,435.8483 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 55.0878 >>>>>>> ACTG content number of A's = 284,326,183 bp (27.41%) number of C's = 235,613,737 bp (22.72%) number of T's = 282,699,988 bp (27.26%) number of G's = 234,310,584 bp (22.59%) number of N's = 203,936 bp (0.02%) GC percentage = 45.31% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 6,058,131 number of insertions = 64,618 mapped reads with insertion percentage = 0.61% number of deletions = 54,481 mapped reads with deletion percentage = 0.51% homopolymer indels = 44.33% >>>>>>> Coverage mean coverageData = 0.3351X std coverageData = 12.7967X There is a 3.25% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.22% of reference with a coverageData >= 16X There is a 0.21% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.19% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.16% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 110537906 0.44348096528914965 19.452543726975897 chr2 243199373 71837381 0.2953847294663872 11.725593370838702 chr3 198022430 131728999 0.6652226164480458 15.469900890167143 chr4 191154276 49762224 0.2603249325168117 10.622686791192885 chr5 180915260 70517515 0.38978201728256645 16.752177844614106 chr6 171115067 59726449 0.3490426065169352 10.003066936489782 chr7 159138663 41679985 0.26190986033356334 7.618574187245877 chr8 146364022 45429693 0.3103883890263688 10.547902016103604 chr9 141213431 56280597 0.3985498872270868 12.124161502880087 chr10 135534747 21527846 0.1588363609812914 6.6783690742502735 chr11 135006516 40706665 0.3015162986651696 9.99766627936944 chr12 133851895 53562129 0.4001596615423338 18.637029128013154 chr13 115169878 18208365 0.15810006328217174 6.247085003570182 chr14 107349540 21116625 0.19670904039272083 7.872548227350961 chr15 102531392 27152933 0.2648255570352541 13.59818042739898 chr16 90354753 52380326 0.5797185456309089 21.591434394092264 chr17 81195210 35945005 0.4426985902247189 12.279211242866051 chr18 78077248 18530367 0.23733376207112217 8.517871133196738 chr19 59128983 29905710 0.5057707486699036 16.359602631473546 chr20 63025520 19444919 0.3085245310153728 10.512447196196954 chr21 48129895 3586135 0.0745095122272758 2.8646665521246693 chr22 51304566 8746467 0.17048125891952776 6.084870824667582 chrMT 16571 3441 0.20765192203246635 0.5403555989643332 chrX 155270560 47650394 0.3068862120417418 9.72723193230551 chrY 59373566 1320724 0.022244309866784825 0.8973989735021413