BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1298936.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 = 168,345,296 number of mapped reads = 162,309,245 (96.41%) number of supplementary alignments = 64,535 (0.04%) number of secondary alignments = 0 number of mapped bases = 16,145,652,002 bp number of sequenced bases = 16,143,091,330 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,102,765 duplication rate = 56.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0227 >>>>>>> ACTG content number of A's = 3,947,460,573 bp (24.45%) number of C's = 4,123,449,124 bp (25.54%) number of T's = 4,023,998,664 bp (24.93%) number of G's = 4,044,492,328 bp (25.05%) number of N's = 3,690,641 bp (0.02%) GC percentage = 50.6% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 111,523,395 number of insertions = 729,285 mapped reads with insertion percentage = 0.44% number of deletions = 1,217,504 mapped reads with deletion percentage = 0.74% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 5.2155X std coverageData = 47.8758X There is a 10.68% of reference with a coverageData >= 1X There is a 7.04% of reference with a coverageData >= 2X There is a 5.87% of reference with a coverageData >= 3X There is a 5.45% of reference with a coverageData >= 4X There is a 5.18% of reference with a coverageData >= 5X There is a 4.99% of reference with a coverageData >= 6X There is a 4.84% of reference with a coverageData >= 7X There is a 4.72% of reference with a coverageData >= 8X There is a 4.62% of reference with a coverageData >= 9X There is a 4.52% of reference with a coverageData >= 10X There is a 4.44% of reference with a coverageData >= 11X There is a 4.37% of reference with a coverageData >= 12X There is a 4.3% of reference with a coverageData >= 13X There is a 4.24% of reference with a coverageData >= 14X There is a 4.18% of reference with a coverageData >= 15X There is a 4.12% of reference with a coverageData >= 16X There is a 4.07% of reference with a coverageData >= 17X There is a 4.02% of reference with a coverageData >= 18X There is a 3.97% of reference with a coverageData >= 19X There is a 3.93% of reference with a coverageData >= 20X There is a 3.88% of reference with a coverageData >= 21X There is a 3.84% of reference with a coverageData >= 22X There is a 3.8% of reference with a coverageData >= 23X There is a 3.76% of reference with a coverageData >= 24X There is a 3.72% of reference with a coverageData >= 25X There is a 3.69% of reference with a coverageData >= 26X There is a 3.65% of reference with a coverageData >= 27X There is a 3.61% of reference with a coverageData >= 28X There is a 3.58% of reference with a coverageData >= 29X There is a 3.55% of reference with a coverageData >= 30X There is a 3.51% of reference with a coverageData >= 31X There is a 3.48% of reference with a coverageData >= 32X There is a 3.45% of reference with a coverageData >= 33X There is a 3.42% of reference with a coverageData >= 34X There is a 3.38% of reference with a coverageData >= 35X There is a 3.35% of reference with a coverageData >= 36X There is a 3.32% of reference with a coverageData >= 37X There is a 3.29% of reference with a coverageData >= 38X There is a 3.26% of reference with a coverageData >= 39X There is a 3.24% of reference with a coverageData >= 40X There is a 3.21% of reference with a coverageData >= 41X There is a 3.18% of reference with a coverageData >= 42X There is a 3.15% of reference with a coverageData >= 43X There is a 3.12% of reference with a coverageData >= 44X There is a 3.09% of reference with a coverageData >= 45X There is a 3.07% of reference with a coverageData >= 46X There is a 3.04% of reference with a coverageData >= 47X There is a 3.01% of reference with a coverageData >= 48X There is a 2.99% of reference with a coverageData >= 49X There is a 2.96% of reference with a coverageData >= 50X There is a 2.93% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1926189706 7.7279233980323765 52.14738405327628 chr2 243199373 840816871 3.4573151263839814 27.502459851704664 chr3 198022430 761345728 3.844744900868048 30.079002205622814 chr4 191154276 476809049 2.4943676855023638 26.260825640884487 chr5 180915260 831694690 4.5971505665138475 53.15280194018431 chr6 171115067 803669072 4.6966587226360375 33.04657381381895 chr7 159138663 1109877110 6.974276954934578 109.6167505090957 chr8 146364022 852336780 5.823403650386158 90.74361585051388 chr9 141213431 629840676 4.460203760646535 31.9114647470039 chr10 135534747 462691594 3.413822685632047 22.975677836099475 chr11 135006516 870094107 6.4448304628496595 36.646501827531395 chr12 133851895 543152704 4.057863386992018 23.540494523237975 chr13 115169878 259759468 2.255446237426769 19.18268491840214 chr14 107349540 471796221 4.394953355179724 30.570755629096578 chr15 102531392 728837309 7.108430840381061 44.19642344220744 chr16 90354753 779709045 8.629419251469814 47.68460636848716 chr17 81195210 688068315 8.474247618794262 43.953085212356704 chr18 78077248 267009693 3.4198143484770367 32.5810918411613 chr19 59128983 1186661035 20.069024948391213 81.84572021864436 chr20 63025520 386162512 6.127081728163449 36.78973779541223 chr21 48129895 221336575 4.598733801517747 41.54722822759335 chr22 51304566 307077393 5.985381359624014 36.082561549184646 chrMT 16571 803471 48.48657292861022 15.476718581284041 chrX 155270560 709974914 4.572501792999265 32.10126405898489 chrY 59373566 29937964 0.5042305190158193 23.695693223123445