BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081215.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,211,433 number of mapped reads = 1,936,186 (87.55%) number of supplementary alignments = 24,275 (1.1%) number of secondary alignments = 0 number of mapped bases = 126,408,761 bp number of sequenced bases = 126,362,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,369 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0795 >>>>>>> ACTG content number of A's = 35,860,107 bp (28.38%) number of C's = 24,649,535 bp (19.51%) number of T's = 38,441,475 bp (30.42%) number of G's = 27,403,431 bp (21.69%) number of N's = 8,197 bp (0.01%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,108,543 number of insertions = 9,370 mapped reads with insertion percentage = 0.48% number of deletions = 28,389 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3103X There is a 3.19% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 11549726 0.04633780230381051 0.4852481328655606 chr2 243199373 9728638 0.04000272648729238 0.3720758452470093 chr3 198022430 8047103 0.04063733083166387 0.24873913013557147 chr4 191154276 4583760 0.023979374649196965 0.19252258937040861 chr5 180915260 7559851 0.041786696158190306 0.2520361304731717 chr6 171115067 10457441 0.06111350206232862 0.33284431550717936 chr7 159138663 8763108 0.05506586416400897 0.40207175614541846 chr8 146364022 8118019 0.05546457994984587 0.36718506012361435 chr9 141213431 3764244 0.026656416272471985 0.2335299719029976 chr10 135534747 3698423 0.02728763716952967 0.25128882049444856 chr11 135006516 6066471 0.044934653376285924 0.30278676172936275 chr12 133851895 3985862 0.02977815144118804 0.21181755803709296 chr13 115169878 3310575 0.028745146365441145 0.2125474871860505 chr14 107349540 4545664 0.042344513073833384 0.26577951715451736 chr15 102531392 2507892 0.024459747898477765 0.21312900637746776 chr16 90354753 5024193 0.05560518769831621 0.2982516206406736 chr17 81195210 2510989 0.030925334142248045 0.22552459126554314 chr18 78077248 2980679 0.03817602536400873 0.3483786773724271 chr19 59128983 3913717 0.06618948612730241 0.4357782717853475 chr20 63025520 3102698 0.04922923285678563 0.28025716469175055 chr21 48129895 2181543 0.04532615331905461 0.2683612796485096 chr22 51304566 942375 0.018368248159432828 0.16360973830388353 chrMT 16571 56401 3.403596644740812 2.9647499345566164 chrX 155270560 8681589 0.05591265337099319 0.3025874472271861 chrY 59373566 327800 0.0055209754455374975 0.09858593483207617