BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008741.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 = 2,327,378 number of mapped reads = 1,622,238 (69.7%) number of supplementary alignments = 6,245 (0.27%) number of secondary alignments = 0 number of mapped bases = 96,371,188 bp number of sequenced bases = 96,313,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,858 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5379 >>>>>>> ACTG content number of A's = 26,819,437 bp (27.85%) number of C's = 16,050,663 bp (16.66%) number of T's = 29,494,668 bp (30.62%) number of G's = 23,936,124 bp (24.85%) number of N's = 12,847 bp (0.01%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 1,088,712 number of insertions = 8,375 mapped reads with insertion percentage = 0.51% number of deletions = 36,635 mapped reads with deletion percentage = 2.23% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0311X std coverageData = 0.2642X There is a 2.66% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 8087529 0.03244737753331415 0.3462732545191832 chr2 243199373 8554626 0.03517536206805928 0.3357214630706612 chr3 198022430 7191891 0.03631856754813079 0.23035990073691712 chr4 191154276 5618267 0.02939127032659212 0.20888167509177033 chr5 180915260 5202862 0.028758558012187584 0.2006319810363867 chr6 171115067 5561514 0.03250160314637869 0.237484824883843 chr7 159138663 5493515 0.03452030384344752 0.3645759838887969 chr8 146364022 6907720 0.04719547813464705 0.3411064373541757 chr9 141213431 3372867 0.02388488811662681 0.2487494755150449 chr10 135534747 4714837 0.03478692441872489 0.26339662242098016 chr11 135006516 4359063 0.03228779713121402 0.2704214650957945 chr12 133851895 4496257 0.03359128385892482 0.22039054363240979 chr13 115169878 2812123 0.024417174428195538 0.1918167096316335 chr14 107349540 3246895 0.030246007574881086 0.21107060861431445 chr15 102531392 2719847 0.026526968442991586 0.19844837658880096 chr16 90354753 2348392 0.025990796521794486 0.20245940720564598 chr17 81195210 2536899 0.031244441636397023 0.22495021005507443 chr18 78077248 2015315 0.025811808838344302 0.36611487262071013 chr19 59128983 1694758 0.02866205224601952 0.25650982408808615 chr20 63025520 1978790 0.03139664694555475 0.21607645021578922 chr21 48129895 1074676 0.022328658726556542 0.18410527521625245 chr22 51304566 1042969 0.020328970329853292 0.16409072344790362 chrMT 16571 38761 2.3390863556816126 2.312847711075972 chrX 155270560 5032927 0.03241391671415367 0.2299884519906852 chrY 59373566 267888 0.0045119068644116815 0.09883547260401594