BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524661.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,369,443 number of mapped reads = 2,193,381 (92.57%) number of supplementary alignments = 9,678 (0.41%) number of secondary alignments = 0 number of mapped bases = 129,557,101 bp number of sequenced bases = 129,519,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,516 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8177 >>>>>>> ACTG content number of A's = 33,609,972 bp (25.95%) number of C's = 23,229,151 bp (17.93%) number of T's = 40,277,846 bp (31.1%) number of G's = 32,384,568 bp (25%) number of N's = 17,579 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 634,420 number of insertions = 7,703 mapped reads with insertion percentage = 0.35% number of deletions = 23,770 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.0419X std coverageData = 0.3744X There is a 3.66% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10431483 0.04185138218772984 0.7001962835552147 chr2 243199373 10895764 0.04480177668879105 0.5197953006513495 chr3 198022430 8551386 0.043183926184523644 0.23306864921879344 chr4 191154276 8354358 0.04370479266704973 0.2707875160198814 chr5 180915260 7834608 0.04330540165600182 0.23390931318716765 chr6 171115067 7352854 0.04297023125380303 0.26986225865457336 chr7 159138663 7081371 0.04449811797149508 0.4334378498602069 chr8 146364022 6641298 0.04537520839650061 0.39494833243513966 chr9 141213431 5444073 0.03855209070021109 0.30748772615364073 chr10 135534747 6320643 0.046634852979804506 0.39365289910296974 chr11 135006516 5962327 0.0441632535721461 0.3195642188287074 chr12 133851895 5818270 0.04346796883226793 0.23635600191558123 chr13 115169878 4026530 0.034961658985173186 0.20905641981854894 chr14 107349540 3882177 0.03616389040884572 0.2202934414391007 chr15 102531392 3792112 0.03698488751620577 0.21606295650427118 chr16 90354753 3788305 0.04192701406643212 0.25113943413999057 chr17 81195210 3550230 0.043724623656986664 0.25476548418204614 chr18 78077248 3413488 0.04371936879742483 0.5721955839233712 chr19 59128983 2710272 0.04583660774277142 0.49263106651929983 chr20 63025520 2763187 0.043842351479210326 0.23837453603093758 chr21 48129895 1711905 0.03556843413018042 0.25473916763224397 chr22 51304566 1555272 0.030314494815139845 0.19537521189577328 chrMT 16571 82044 4.951059079114115 3.456229336228044 chrX 155270560 7165077 0.04614575358007339 0.2693151696806593 chrY 59373566 428067 0.007209723599892922 0.26309362917488766