BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867861.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 = 2,008,986 number of mapped reads = 1,861,544 (92.66%) number of supplementary alignments = 8,339 (0.42%) number of secondary alignments = 0 number of mapped bases = 110,324,787 bp number of sequenced bases = 110,290,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,002 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9108 >>>>>>> ACTG content number of A's = 28,711,003 bp (26.03%) number of C's = 19,841,916 bp (17.99%) number of T's = 34,270,726 bp (31.07%) number of G's = 27,452,384 bp (24.89%) number of N's = 14,363 bp (0.01%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 548,862 number of insertions = 9,443 mapped reads with insertion percentage = 0.5% number of deletions = 21,491 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.5% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.3356X There is a 3.11% of reference with a coverageData >= 1X There is a 0.33% 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% 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 8831549 0.03543240520151001 0.6074443389728106 chr2 243199373 9378709 0.03856386998168782 0.4521131796067555 chr3 198022430 7285005 0.036788787007613226 0.21391729432901607 chr4 191154276 7032529 0.03678980741189384 0.2517362362859253 chr5 180915260 6659813 0.036811781383173536 0.2158064513072686 chr6 171115067 6301457 0.0368258453827447 0.243634045171539 chr7 159138663 6051762 0.03802823202052414 0.3905586722351982 chr8 146364022 5615659 0.038367755431044384 0.3959678784098712 chr9 141213431 4686927 0.03319037691251903 0.27570425718152153 chr10 135534747 5344087 0.03942964529974 0.3497235267108117 chr11 135006516 5009484 0.037105497930188795 0.2890210619921996 chr12 133851895 4943635 0.03693361980418731 0.2170222157252368 chr13 115169878 3474742 0.030170579845539128 0.19504533599012566 chr14 107349540 3375389 0.03144297590842029 0.20750053402016252 chr15 102531392 3184863 0.031062320893878042 0.19719604010300612 chr16 90354753 3199533 0.035410787963749954 0.22858559744639528 chr17 81195210 3033085 0.037355467151325795 0.2354195012500663 chr18 78077248 2954859 0.037845327232845095 0.5072696951907288 chr19 59128983 2307781 0.03902960752766541 0.4487667499350488 chr20 63025520 2341677 0.03715442569930403 0.22121094768792354 chr21 48129895 1477144 0.03069077960797546 0.2443592598377418 chr22 51304566 1316091 0.02565251209804601 0.17950009475143827 chrMT 16571 35662 2.1520728984370288 1.9651185543005882 chrX 155270560 6105819 0.03932373915570344 0.24663955920388472 chrY 59373566 377526 0.00635848619906037 0.2445369735044291