BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506088.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 14,647,978 number of mapped reads = 12,035,141 (82.16%) number of supplementary alignments = 194,283 (1.33%) number of secondary alignments = 0 number of mapped bases = 944,191,449 bp number of sequenced bases = 943,811,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,390,671 duplication rate = 13.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5746 >>>>>>> ACTG content number of A's = 253,314,808 bp (26.84%) number of C's = 179,196,973 bp (18.99%) number of T's = 275,005,281 bp (29.14%) number of G's = 236,156,379 bp (25.02%) number of N's = 138,257 bp (0.01%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 7,350,762 number of insertions = 75,349 mapped reads with insertion percentage = 0.61% number of deletions = 185,796 mapped reads with deletion percentage = 1.51% homopolymer indels = 42.3% >>>>>>> Coverage mean coverageData = 0.305X std coverageData = 1.8813X There is a 14.91% of reference with a coverageData >= 1X There is a 6.67% of reference with a coverageData >= 2X There is a 3.37% of reference with a coverageData >= 3X There is a 1.84% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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% 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 72855958 0.2923000059446191 3.4777663758353117 chr2 243199373 80788713 0.3321912881740859 2.114990095018979 chr3 198022430 60122482 0.30361450468010115 0.9850802659993667 chr4 191154276 58667564 0.3069121195070729 1.7382760422981625 chr5 180915260 72879085 0.40283547667565467 1.198893782945574 chr6 171115067 37599799 0.21973400507156976 0.993019624059513 chr7 159138663 45901322 0.2884360163312419 1.9295246119712577 chr8 146364022 56801306 0.38808243463000763 2.1360945077894558 chr9 141213431 27944609 0.19788917245414142 1.7585665282329 chr10 135534747 50686627 0.3739751474948339 2.4463235953658384 chr11 135006516 40538219 0.3002686107387587 1.6997260956985798 chr12 133851895 37640388 0.2812092275570697 1.00082135986833 chr13 115169878 19781989 0.1717635665117228 0.7240170391142652 chr14 107349540 25148481 0.2342672451134863 1.1113705674169714 chr15 102531392 31937049 0.31148556921962006 1.064110905534137 chr16 90354753 34484915 0.38166132776656475 1.5097920184094884 chr17 81195210 23578773 0.2903961083418591 1.2658301826886365 chr18 78077248 17206248 0.22037467304175476 2.747345237263064 chr19 59128983 24852365 0.4203076687451228 2.724301056581398 chr20 63025520 27600641 0.4379280170952973 1.3717695171369235 chr21 48129895 14877183 0.309104829752901 1.6119430434673139 chr22 51304566 9928873 0.1935280575222096 0.9659969093821597 chrMT 16571 406941 24.557419588437632 15.648419901000183 chrX 155270560 68339907 0.44013435000170026 1.4600117801424166 chrY 59373566 3622012 0.06100378070604686 2.226264947806968