BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046484.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 13,437,376 number of mapped reads = 13,380,799 (99.58%) number of supplementary alignments = 49,787 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,703,201 number of mapped paired reads (second in pair) = 6,677,598 number of mapped paired reads (both in pair) = 13,342,146 number of mapped paired reads (singletons) = 38,653 number of mapped bases = 1,318,158,167 bp number of sequenced bases = 1,317,779,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,950,199 duplication rate = 22.32% >>>>>>> Insert size mean insert size = 18,259.225 std insert size = 1,275,439.8931 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 53.1778 >>>>>>> ACTG content number of A's = 333,739,383 bp (25.33%) number of C's = 325,000,045 bp (24.66%) number of T's = 332,147,772 bp (25.21%) number of G's = 326,773,653 bp (24.8%) number of N's = 118,858 bp (0.01%) GC percentage = 49.46% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 6,002,500 number of insertions = 130,443 mapped reads with insertion percentage = 0.95% number of deletions = 120,807 mapped reads with deletion percentage = 0.88% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 0.4258X std coverageData = 59.6592X There is a 3.92% of reference with a coverageData >= 1X There is a 2.36% of reference with a coverageData >= 2X There is a 1.29% of reference with a coverageData >= 3X There is a 0.86% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% 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 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 214074950 0.8588742894245387 68.8705868248705 chr2 243199373 105908496 0.4354801358801201 64.27795878829286 chr3 198022430 28807294 0.14547490402981117 6.848099098570252 chr4 191154276 24337596 0.12731912939263781 17.37585503471447 chr5 180915260 109974293 0.607877373086162 65.62851783358339 chr6 171115067 43223403 0.2525984634655229 24.311823026125005 chr7 159138663 153629325 0.9653802671447604 143.11818691416462 chr8 146364022 38303003 0.2616968465105448 38.67591749546217 chr9 141213431 16066549 0.11377493547338284 5.4251425223833785 chr10 135534747 36223588 0.2672642167546895 14.325378498884083 chr11 135006516 29647645 0.21960158574864638 21.357263372884958 chr12 133851895 162750211 1.215897697974317 90.08728294267516 chr13 115169878 9986112 0.08670767194873645 3.2109318645960183 chr14 107349540 46342326 0.4316956178852746 51.90066958531576 chr15 102531392 20187996 0.1968957565698513 11.969185285705858 chr16 90354753 12611874 0.1395817439731145 4.595969558977937 chr17 81195210 126509232 1.5580873797850883 85.30362651128185 chr18 78077248 6653851 0.08522138229052335 2.3674726262109265 chr19 59128983 21350369 0.36108128225374686 18.253017484560836 chr20 63025520 20610050 0.3270111853103314 26.90808785578437 chr21 48129895 1611765 0.033487814590079615 1.1051332901980977 chr22 51304566 12265952 0.23908109855173515 21.29704677348141 chrMT 16571 282492 17.0473719147909 6.515010969543289 chrX 155270560 76565081 0.49310752147734893 120.06027935814579 chrY 59373566 234714 0.003953173370115583 0.17506425036820566