BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124909.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,610,214 number of mapped reads = 4,510,879 (97.85%) number of supplementary alignments = 37,631 (0.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,260,932 number of mapped paired reads (second in pair) = 2,249,947 number of mapped paired reads (both in pair) = 4,478,762 number of mapped paired reads (singletons) = 32,117 number of mapped bases = 392,262,868 bp number of sequenced bases = 391,971,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 519,029 duplication rate = 7.22% >>>>>>> Insert size mean insert size = 62,111.6183 std insert size = 2,286,992.5644 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.4182 >>>>>>> ACTG content number of A's = 109,631,830 bp (27.97%) number of C's = 74,161,966 bp (18.92%) number of T's = 115,896,794 bp (29.57%) number of G's = 92,275,337 bp (23.54%) number of N's = 5,499 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,361,446 number of insertions = 70,932 mapped reads with insertion percentage = 1.5% number of deletions = 150,552 mapped reads with deletion percentage = 3.25% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.1267X std coverageData = 1.5731X There is a 7.97% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 31261057 0.1254201769872421 1.3486622450408228 chr2 243199373 27492108 0.11304349867711214 2.9424492467255523 chr3 198022430 33473659 0.16903973453916307 0.5995525589583343 chr4 191154276 23688540 0.12392367304407044 1.4096577393859935 chr5 180915260 20790071 0.11491607175646765 0.5707528140510869 chr6 171115067 24472314 0.14301671050393241 1.0587878608340373 chr7 159138663 22302487 0.1401449941803269 1.1648406434713006 chr8 146364022 26789272 0.18303181091866963 0.7914107896889994 chr9 141213431 13062496 0.0925017960933192 1.5457710496478512 chr10 135534747 23190724 0.17110537713255183 3.427007289746474 chr11 135006516 18060690 0.13377643194644026 0.7660328031286869 chr12 133851895 16206346 0.12107670197721146 0.4993074392630182 chr13 115169878 7864016 0.06828188183024732 0.37121063559444506 chr14 107349540 14101233 0.13135811294580302 0.6114245438480702 chr15 102531392 7621131 0.07432973308311273 0.3811891701199002 chr16 90354753 11982163 0.13261242604470402 2.2663340907114544 chr17 81195210 11857993 0.1460430116505641 1.094386234514029 chr18 78077248 8095287 0.10368304733281583 1.6067717223206281 chr19 59128983 6456524 0.10919389565688961 0.9811872185432117 chr20 63025520 10337426 0.16401968599386407 0.730917728928562 chr21 48129895 5857035 0.12169224553679163 1.1066513928961978 chr22 51304566 4235464 0.08255530316736331 0.5388113949799495 chrMT 16571 1610954 97.21525556695431 59.18326244193197 chrX 155270560 13928906 0.0897073212075747 0.6197733884094444 chrY 59373566 7524972 0.126739431483701 3.6150038297665334