BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472514.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,402,232 number of mapped reads = 18,215,788 (98.99%) number of supplementary alignments = 75,330 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,132,352 number of mapped paired reads (second in pair) = 9,083,436 number of mapped paired reads (both in pair) = 18,119,362 number of mapped paired reads (singletons) = 96,426 number of mapped bases = 1,790,530,363 bp number of sequenced bases = 1,790,292,529 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,480,715 duplication rate = 46.45% >>>>>>> Insert size mean insert size = 29,060.1477 std insert size = 1,675,873.5185 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 55.2523 >>>>>>> ACTG content number of A's = 494,217,246 bp (27.61%) number of C's = 403,766,712 bp (22.55%) number of T's = 490,653,158 bp (27.41%) number of G's = 401,376,871 bp (22.42%) number of N's = 278,542 bp (0.02%) GC percentage = 44.97% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 10,449,706 number of insertions = 99,238 mapped reads with insertion percentage = 0.54% number of deletions = 94,433 mapped reads with deletion percentage = 0.51% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.5784X std coverageData = 18.8869X There is a 5.76% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.08% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 200145099 0.8029873634697985 27.693787904594902 chr2 243199373 104836548 0.43107244359548574 13.181416456151032 chr3 198022430 224565812 1.1340423001576134 26.44992545461556 chr4 191154276 88245677 0.4616463667284116 17.652029478324433 chr5 180915260 79749328 0.44081039929965 15.493632425626714 chr6 171115067 100150538 0.585281820916448 16.00957069626667 chr7 159138663 87296985 0.548559246095966 16.829025544360082 chr8 146364022 87475605 0.5976578383449999 18.911774821976824 chr9 141213431 94930794 0.6722504603687449 17.35186692980828 chr10 135534747 50959248 0.3759865947881247 12.478109858980483 chr11 135006516 72582115 0.5376193472024713 15.598987243183869 chr12 133851895 93609944 0.6993546411875603 23.25910165794578 chr13 115169878 41791533 0.3628686052788907 14.805889565045893 chr14 107349540 55239620 0.5145771467674664 16.994725754180543 chr15 102531392 36305181 0.35408844346909873 10.156721999999553 chr16 90354753 62225420 0.6886789895823189 23.062188340175965 chr17 81195210 61407017 0.7562886653042711 18.944419763703177 chr18 78077248 37275460 0.4774176979188611 18.22010150185048 chr19 59128983 34003620 0.5750753399563797 15.723034568052421 chr20 63025520 41636711 0.6606325659827955 22.31899217644662 chr21 48129895 8584097 0.1783527057351777 6.8619304769506995 chr22 51304566 19639600 0.38280413482106057 9.933204651019867 chrMT 16571 4539 0.2739122563514574 0.802796402052047 chrX 155270560 105477045 0.6793112937829296 24.807274104808503 chrY 59373566 2392827 0.04030121754856362 1.793210724643203