BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818786.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,264,005 number of mapped reads = 2,201,494 (97.24%) number of supplementary alignments = 17,238 (0.76%) number of secondary alignments = 0 number of mapped bases = 149,537,132 bp number of sequenced bases = 149,473,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,086,399 duplication rate = 41.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7461 >>>>>>> ACTG content number of A's = 44,621,924 bp (29.85%) number of C's = 31,597,285 bp (21.14%) number of T's = 41,183,843 bp (27.55%) number of G's = 32,061,318 bp (21.45%) number of N's = 8,991 bp (0.01%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 756,018 number of insertions = 21,788 mapped reads with insertion percentage = 0.98% number of deletions = 38,655 mapped reads with deletion percentage = 1.74% homopolymer indels = 40.74% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.6043X There is a 2.07% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% 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% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 12187290 0.04889572572017784 0.7692377752086486 chr2 243199373 13235810 0.05442370116636773 1.032274413715966 chr3 198022430 10250913 0.05176642363190877 0.44188766065074814 chr4 191154276 9855363 0.051557115049835456 0.5145988689036668 chr5 180915260 9374252 0.051815706425207025 0.45697373078385334 chr6 171115067 8820288 0.0515459459803151 0.5011504298770885 chr7 159138663 8239450 0.05177528731657121 0.5323663514215342 chr8 146364022 7740734 0.05288686313908482 0.5044199636583027 chr9 141213431 6406239 0.045365649390673043 0.4916542254288249 chr10 135534747 7211246 0.05320588380188587 0.6481308424570272 chr11 135006516 6942294 0.05142191803542282 0.5074361474987943 chr12 133851895 6720017 0.050204870091678566 0.4825614726968465 chr13 115169878 4812210 0.04178358164102596 0.39694055295853886 chr14 107349540 4654596 0.043359254264154275 0.4745259393964401 chr15 102531392 4246557 0.04141713983557348 0.39719101501065307 chr16 90354753 4390463 0.04859138954206427 0.7240554072765331 chr17 81195210 3958744 0.048755881042736385 0.46004057687608657 chr18 78077248 4082861 0.052292583365643214 0.6518658379741042 chr19 59128983 2964529 0.050136647877065635 0.6721634434595879 chr20 63025520 3262683 0.05176764904121378 0.47419511356654914 chr21 48129895 2013668 0.04183819640578896 0.4241110457634159 chr22 51304566 1800921 0.035102548182553574 0.40270150140986477 chrMT 16571 175349 10.581678836521634 12.046957158744378 chrX 155270560 4709436 0.030330514683530478 0.3824379091026527 chrY 59373566 1481219 0.024947448836069572 1.1116125301365596