BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472423.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 = 30,909,406 number of mapped reads = 30,612,991 (99.04%) number of supplementary alignments = 115,136 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,348,945 number of mapped paired reads (second in pair) = 15,264,046 number of mapped paired reads (both in pair) = 30,460,918 number of mapped paired reads (singletons) = 152,073 number of mapped bases = 2,997,247,609 bp number of sequenced bases = 2,996,897,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,616,118 duplication rate = 49.58% >>>>>>> Insert size mean insert size = 17,841.3805 std insert size = 1,325,841.2065 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 55.1914 >>>>>>> ACTG content number of A's = 817,120,149 bp (27.27%) number of C's = 683,492,079 bp (22.81%) number of T's = 817,493,379 bp (27.28%) number of G's = 678,415,604 bp (22.64%) number of N's = 376,397 bp (0.01%) GC percentage = 45.44% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 16,131,435 number of insertions = 176,058 mapped reads with insertion percentage = 0.57% number of deletions = 149,815 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.9682X std coverageData = 26.9786X There is a 8.13% of reference with a coverageData >= 1X There is a 3.55% of reference with a coverageData >= 2X There is a 1.39% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.53% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.48% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.42% of reference with a coverageData >= 14X There is a 0.41% of reference with a coverageData >= 15X There is a 0.4% of reference with a coverageData >= 16X There is a 0.4% of reference with a coverageData >= 17X There is a 0.39% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.38% of reference with a coverageData >= 20X There is a 0.37% of reference with a coverageData >= 21X There is a 0.37% of reference with a coverageData >= 22X There is a 0.36% of reference with a coverageData >= 23X There is a 0.36% of reference with a coverageData >= 24X There is a 0.35% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.33% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.32% of reference with a coverageData >= 33X There is a 0.31% of reference with a coverageData >= 34X There is a 0.31% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.29% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.28% of reference with a coverageData >= 45X There is a 0.28% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 333679141 1.3387294268767338 38.00295249886479 chr2 243199373 227673887 0.9361614883768635 26.139357789345407 chr3 198022430 263536232 1.3308403093528345 26.40028399840414 chr4 191154276 92493451 0.48386807209062904 18.367218596920175 chr5 180915260 128831779 0.7121111784600149 20.481286980466674 chr6 171115067 229987398 1.3440511232128962 29.75048315256339 chr7 159138663 179700615 1.1292077714640596 28.335771935518334 chr8 146364022 166280832 1.136077225317025 27.379055721517105 chr9 141213431 130405879 0.9234665433488405 24.08156230496451 chr10 135534747 77768654 0.5737912654974004 18.57397221938365 chr11 135006516 98150685 0.7270070209055688 21.258695150306416 chr12 133851895 139480699 1.0420524789731218 23.471752320004114 chr13 115169878 83022131 0.7208667096096082 22.633735615879143 chr14 107349540 82133674 0.7651050391086911 21.375902934656892 chr15 102531392 75140434 0.7328529588284532 20.096779251576514 chr16 90354753 188396840 2.0850794644970145 60.05666386596731 chr17 81195210 109756302 1.3517583364831496 25.463729287710752 chr18 78077248 31099447 0.39831638277004844 14.15243240236805 chr19 59128983 80731638 1.3653479884813848 28.33024570237799 chr20 63025520 100196406 1.5897751577456243 41.73910931017093 chr21 48129895 26642175 0.5535473326920826 27.17874947181622 chr22 51304566 23346208 0.4550512716548465 10.319997229965349 chrMT 16571 7008 0.42290748898678415 0.836103170841607 chrX 155270560 127044405 0.8182130920375376 18.610228965066643 chrY 59373566 1741689 0.029334417946195113 1.5444279190348484