BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063521.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 = 4,470,074 number of mapped reads = 4,229,257 (94.61%) number of supplementary alignments = 29,118 (0.65%) number of secondary alignments = 0 number of mapped bases = 270,838,064 bp number of sequenced bases = 270,722,800 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 528,035 duplication rate = 10.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8734 >>>>>>> ACTG content number of A's = 69,406,011 bp (25.64%) number of C's = 48,653,115 bp (17.97%) number of T's = 88,343,670 bp (32.63%) number of G's = 64,290,521 bp (23.75%) number of N's = 29,483 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,427,227 number of insertions = 15,865 mapped reads with insertion percentage = 0.37% number of deletions = 65,294 mapped reads with deletion percentage = 1.53% homopolymer indels = 44.2% >>>>>>> Coverage mean coverageData = 0.0875X std coverageData = 0.9547X There is a 6.39% of reference with a coverageData >= 1X There is a 1.55% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 27934672 0.11207463350713176 2.324957393584499 chr2 243199373 26995562 0.1110017746632924 1.4255205537855589 chr3 198022430 18188447 0.09185043835690734 0.394595594771569 chr4 191154276 14745453 0.07713901728256395 0.37503821323655806 chr5 180915260 14587776 0.08063319810611885 0.37149372044327 chr6 171115067 21026436 0.12287892801397787 0.6487302287614392 chr7 159138663 27383177 0.1720711766945032 1.236044514752795 chr8 146364022 9011917 0.06157194149802743 0.7728366592991465 chr9 141213431 7707889 0.054583257027442385 0.5043924817659198 chr10 135534747 15907606 0.11736920865023638 0.6540877369910646 chr11 135006516 10102361 0.07482869197217118 0.4974339213394909 chr12 133851895 12069909 0.09017361315654142 0.43175461955884575 chr13 115169878 4949634 0.04297681030798695 0.33467965776751685 chr14 107349540 2054881 0.0191419637196396 0.2666763370255714 chr15 102531392 5150542 0.05023380546711002 0.3557892487108194 chr16 90354753 4609497 0.051015545358194934 0.33011307853039484 chr17 81195210 7890885 0.09718411960508508 0.4341135546369938 chr18 78077248 6348744 0.0813136241687207 1.0285434156359343 chr19 59128983 5806872 0.0982068641363238 1.3894348772956695 chr20 63025520 1208180 0.019169695069552777 0.21763235330525932 chr21 48129895 3799640 0.07894552855351128 0.37063201351007374 chr22 51304566 2815128 0.05487090564219957 0.2975158165852283 chrMT 16571 498345 30.073320861746424 15.23018291232164 chrX 155270560 19387458 0.12486242079631837 0.5528667143355317 chrY 59373566 657053 0.011066423061063908 0.22487466240459444