BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 384,154 number of mapped reads = 365,771 (95.21%) number of supplementary alignments = 3,941 (1.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 183,546 number of mapped paired reads (second in pair) = 182,225 number of mapped paired reads (both in pair) = 363,758 number of mapped paired reads (singletons) = 2,013 number of mapped bases = 52,303,168 bp number of sequenced bases = 52,195,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 364,937 duplication rate = 58.68% >>>>>>> Insert size mean insert size = 3,277.5312 std insert size = 510,059.1933 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 11.1371 >>>>>>> ACTG content number of A's = 14,431,418 bp (27.65%) number of C's = 11,193,190 bp (21.44%) number of T's = 14,890,108 bp (28.53%) number of G's = 11,680,617 bp (22.38%) number of N's = 510 bp (0%) GC percentage = 43.82% >>>>>>> Mismatches and indels general error rate = 0.0171 number of mismatches = 845,652 number of insertions = 18,032 mapped reads with insertion percentage = 4.86% number of deletions = 42,498 mapped reads with deletion percentage = 11.4% homopolymer indels = 54.93% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 25.9256X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 199533 8.005316062983851E-4 0.5092891554911917 chr2 243199373 158624 6.52238523657707E-4 0.6383219272453162 chr3 198022430 144769 7.310737475547594E-4 0.24967862499526833 chr4 191154276 5006 2.6188271090519577E-5 0.011139460908922838 chr5 180915260 9208 5.089675685732646E-5 0.03400426650765538 chr6 171115067 4610 2.6940935598616806E-5 0.015877062413761755 chr7 159138663 170555 0.0010717382990706665 1.0323546680438038 chr8 146364022 552976 0.0037780869399721743 3.1797263724607983 chr9 141213431 29983 2.123239962918258E-4 0.18767648763829103 chr10 135534747 2014 1.4859658091957777E-5 0.006356312130335061 chr11 135006516 421951 0.0031254121097384663 2.40463505654041 chr12 133851895 23847 1.7815959945878987E-4 0.15754257108006023 chr13 115169878 42192 3.66345790519983E-4 0.3271372194502416 chr14 107349540 2430 2.2636333607018717E-5 0.014543525502761483 chr15 102531392 11297 1.1018088977081282E-4 0.058122479061832384 chr16 90354753 2280 2.523386899192785E-5 0.008635513106633705 chr17 81195210 1687 2.077708771244018E-5 0.007756495078142954 chr18 78077248 3091 3.958899780893917E-5 0.022964894637887385 chr19 59128983 460 7.779602771114802E-6 0.0032013622912328453 chr20 63025520 2683 4.2570057335504726E-5 0.0170179624674812 chr21 48129895 305268 0.0063425860372228115 3.2793431367724915 chr22 51304566 890 1.7347383856633737E-5 0.01509485549148375 chrMT 16571 48417498 2921.8211333051718 10777.153888580337 chrX 155270560 1788384 0.011517856314809453 8.659287051933738 chrY 59373566 1932 3.253973325435767E-5 0.01219086882549916