BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234072.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,848,014 number of mapped reads = 5,539,939 (94.73%) number of supplementary alignments = 33,588 (0.57%) number of secondary alignments = 0 number of mapped bases = 356,186,433 bp number of sequenced bases = 356,049,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 575,655 duplication rate = 8.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8112 >>>>>>> ACTG content number of A's = 90,560,041 bp (25.43%) number of C's = 65,429,686 bp (18.38%) number of T's = 114,723,836 bp (32.22%) number of G's = 85,302,025 bp (23.96%) number of N's = 34,127 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,897,770 number of insertions = 23,462 mapped reads with insertion percentage = 0.42% number of deletions = 78,245 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.1151X std coverageData = 1.1418X There is a 8.58% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 55202126 0.22147237097555716 2.5726014514694366 chr2 243199373 48744364 0.20042964502215227 2.1381267788241956 chr3 198022430 31433470 0.1587369168230084 0.5107777854151974 chr4 191154276 12918354 0.06758077438979183 0.372462160344224 chr5 180915260 12460896 0.0688769758836264 0.3582435635813653 chr6 171115067 6469281 0.0378066123189491 0.5201505959310547 chr7 159138663 13276259 0.08342572917054104 0.7379403007542534 chr8 146364022 10516483 0.07185155789173381 1.0349448210417105 chr9 141213431 18248885 0.12922910286061953 0.7845793825216838 chr10 135534747 10965341 0.0809042791071134 0.624625359420615 chr11 135006516 15176732 0.11241481114881892 0.7674316648938881 chr12 133851895 9256231 0.0691527826333725 0.36466563395083734 chr13 115169878 16399577 0.14239467198185277 0.5357163644893149 chr14 107349540 14158930 0.13189558148083355 0.5237088327070294 chr15 102531392 13172859 0.12847634995533855 0.5073770058186913 chr16 90354753 12490703 0.13824068557854394 0.5762078747025372 chr17 81195210 13630856 0.16787758785278098 0.6612692407051307 chr18 78077248 10453888 0.13389160437621983 1.8522052912329645 chr19 59128983 10149042 0.17164242449426198 1.5777702415683839 chr20 63025520 6442556 0.10222138587670518 0.47396342329902325 chr21 48129895 6451203 0.1340373379164862 0.4925329462854596 chr22 51304566 5155694 0.10049191333184652 0.39657917310693336 chrMT 16571 295497 17.832176694224852 10.860451092933035 chrX 155270560 2124065 0.013679766466997994 0.36793430650254233 chrY 59373566 593141 0.009989984431792425 0.2529694484439091