BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153392.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 = 72,272,052 number of mapped reads = 71,714,379 (99.23%) number of supplementary alignments = 399,744 (0.55%) number of secondary alignments = 0 number of mapped bases = 6,986,919,634 bp number of sequenced bases = 6,986,144,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,801,968 duplication rate = 43.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3716 >>>>>>> ACTG content number of A's = 1,722,786,975 bp (24.66%) number of C's = 1,768,938,625 bp (25.32%) number of T's = 1,722,084,918 bp (24.65%) number of G's = 1,771,388,392 bp (25.36%) number of N's = 945,563 bp (0.01%) GC percentage = 50.68% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 20,073,735 number of insertions = 507,454 mapped reads with insertion percentage = 0.7% number of deletions = 328,379 mapped reads with deletion percentage = 0.45% homopolymer indels = 45.09% >>>>>>> Coverage mean coverageData = 2.257X std coverageData = 29.5719X There is a 8.84% of reference with a coverageData >= 1X There is a 5.86% of reference with a coverageData >= 2X There is a 4.35% of reference with a coverageData >= 3X There is a 3.86% of reference with a coverageData >= 4X There is a 3.48% of reference with a coverageData >= 5X There is a 3.24% of reference with a coverageData >= 6X There is a 3.05% of reference with a coverageData >= 7X There is a 2.89% of reference with a coverageData >= 8X There is a 2.75% of reference with a coverageData >= 9X There is a 2.64% of reference with a coverageData >= 10X There is a 2.53% of reference with a coverageData >= 11X There is a 2.44% of reference with a coverageData >= 12X There is a 2.35% of reference with a coverageData >= 13X There is a 2.27% of reference with a coverageData >= 14X There is a 2.2% of reference with a coverageData >= 15X There is a 2.13% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 2.01% of reference with a coverageData >= 18X There is a 1.95% of reference with a coverageData >= 19X There is a 1.9% of reference with a coverageData >= 20X There is a 1.85% of reference with a coverageData >= 21X There is a 1.81% of reference with a coverageData >= 22X There is a 1.76% of reference with a coverageData >= 23X There is a 1.72% of reference with a coverageData >= 24X There is a 1.68% of reference with a coverageData >= 25X There is a 1.64% of reference with a coverageData >= 26X There is a 1.6% of reference with a coverageData >= 27X There is a 1.57% of reference with a coverageData >= 28X There is a 1.53% of reference with a coverageData >= 29X There is a 1.5% of reference with a coverageData >= 30X There is a 1.47% of reference with a coverageData >= 31X There is a 1.44% of reference with a coverageData >= 32X There is a 1.41% of reference with a coverageData >= 33X There is a 1.38% of reference with a coverageData >= 34X There is a 1.36% of reference with a coverageData >= 35X There is a 1.33% of reference with a coverageData >= 36X There is a 1.3% of reference with a coverageData >= 37X There is a 1.28% of reference with a coverageData >= 38X There is a 1.26% of reference with a coverageData >= 39X There is a 1.23% of reference with a coverageData >= 40X There is a 1.21% of reference with a coverageData >= 41X There is a 1.19% of reference with a coverageData >= 42X There is a 1.17% of reference with a coverageData >= 43X There is a 1.15% of reference with a coverageData >= 44X There is a 1.13% of reference with a coverageData >= 45X There is a 1.11% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.07% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 1.04% of reference with a coverageData >= 50X There is a 1.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 868857855 3.4858804022799204 33.88293917595199 chr2 243199373 360415657 1.481976094568303 17.763675859197626 chr3 198022430 334183413 1.6876038386156558 19.041812834261556 chr4 191154276 249184387 1.3035773628208034 18.92094086356337 chr5 180915260 437835039 2.42011115590802 40.15198765648698 chr6 171115067 361699977 2.1137821662425553 25.13739553444652 chr7 159138663 411397162 2.5851490407456796 33.332112839087024 chr8 146364022 174715470 1.1937050349709575 22.97164369865605 chr9 141213431 352323950 2.494974787490292 29.204484453507316 chr10 135534747 179267897 1.3226711302305378 15.977161214377304 chr11 135006516 416155939 3.0824878037738563 29.355014300976954 chr12 133851895 264048566 1.9726920265118397 22.60174490558972 chr13 115169878 151612215 1.316422467687254 19.830870692940213 chr14 107349540 131302628 1.2231317246445583 16.200356592754563 chr15 102531392 325861758 3.178165746545214 33.468028412286685 chr16 90354753 307763643 3.406169933307216 31.118263954297248 chr17 81195210 406739832 5.009406737170826 39.64197240144054 chr18 78077248 40377969 0.5171541010256919 8.572951164521475 chr19 59128983 366765988 6.2028123839031695 43.731941969889164 chr20 63025520 176747337 2.804377290342071 28.185853526779205 chr21 48129895 110114986 2.287870896040808 94.64349927581559 chr22 51304566 116852110 2.2776161872220104 24.149559771573706 chrMT 16571 704 0.04248385734113813 0.22000753829117928 chrX 155270560 437888924 2.8201670941355528 33.23247830815299 chrY 59373566 4806228 0.08094895293976448 5.687214219138228