BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234080.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 = 1,076,613 number of mapped reads = 669,893 (62.22%) number of supplementary alignments = 4,450 (0.41%) number of secondary alignments = 0 number of mapped bases = 43,362,874 bp number of sequenced bases = 43,339,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,412 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7946 >>>>>>> ACTG content number of A's = 12,365,762 bp (28.53%) number of C's = 7,239,139 bp (16.7%) number of T's = 14,036,173 bp (32.39%) number of G's = 9,694,064 bp (22.37%) number of N's = 3,868 bp (0.01%) GC percentage = 39.07% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 441,369 number of insertions = 3,956 mapped reads with insertion percentage = 0.59% number of deletions = 13,578 mapped reads with deletion percentage = 2% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 0.1824X There is a 1.27% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 5163635 0.020716638455235786 0.3294040228357763 chr2 243199373 1985182 0.008162775978867347 0.16343821349070808 chr3 198022430 5702748 0.028798495200770942 0.1869154483709191 chr4 191154276 1884266 0.009857304996933472 0.11046389819161266 chr5 180915260 2300923 0.01271823615100241 0.12248338421532612 chr6 171115067 2158087 0.012611905180740162 0.13214581930448643 chr7 159138663 1378407 0.008661672619431269 0.12045480723126122 chr8 146364022 2956292 0.02019821510507548 0.3864812317586386 chr9 141213431 1496601 0.01059814912364816 0.12625898346852288 chr10 135534747 2087159 0.01539943849232994 0.15045762625688838 chr11 135006516 1680584 0.012448169538720634 0.13621416224192778 chr12 133851895 1200844 0.00897143817052422 0.10475565077476164 chr13 115169878 2515312 0.02184001618895524 0.16104047372510458 chr14 107349540 1473161 0.013723030392119053 0.13195255124798336 chr15 102531392 643159 0.006272800821820502 0.08643823724160332 chr16 90354753 1220790 0.01351107672221737 0.14175422042459218 chr17 81195210 820902 0.010110226945653568 0.11054975175853282 chr18 78077248 951789 0.012190350254148302 0.2241250399691147 chr19 59128983 1272687 0.021523911547743007 0.21453740561192278 chr20 63025520 977148 0.015504005361637634 0.14497150466027167 chr21 48129895 866139 0.017995863070135516 0.14711414376272758 chr22 51304566 389239 0.007586829601092425 0.09387113239226078 chrMT 16571 35403 2.136443183875445 2.328650739734701 chrX 155270560 2092211 0.01347461489158022 0.13117561305353295 chrY 59373566 110206 0.0018561458814853734 0.055204925332585864