BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013248.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 = 1,257,792 number of mapped reads = 1,032,145 (82.06%) number of supplementary alignments = 14,755 (1.17%) number of secondary alignments = 0 number of mapped bases = 65,581,924 bp number of sequenced bases = 65,510,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,661 duplication rate = 10.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6673 >>>>>>> ACTG content number of A's = 18,620,387 bp (28.42%) number of C's = 11,251,693 bp (17.18%) number of T's = 21,751,535 bp (33.2%) number of G's = 13,873,667 bp (21.18%) number of N's = 13,580 bp (0.02%) GC percentage = 38.35% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 678,847 number of insertions = 5,138 mapped reads with insertion percentage = 0.49% number of deletions = 40,592 mapped reads with deletion percentage = 3.85% homopolymer indels = 42.04% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.3072X There is a 1.24% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% 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% 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 968580 0.003885968252010895 0.151059351904468 chr2 243199373 14208563 0.05842351822181713 0.44202172554638747 chr3 198022430 5043639 0.025470038924378414 0.24620814000807784 chr4 191154276 8468944 0.04430423518226712 0.34687968758491705 chr5 180915260 2301339 0.0127205355700785 0.16843946206951457 chr6 171115067 788669 0.004608997990808139 0.10857183630207559 chr7 159138663 8000424 0.05027328902467906 0.5937413293197892 chr8 146364022 4990657 0.034097566682063436 0.6850402936389808 chr9 141213431 1944547 0.01377026948661845 0.24292778009716934 chr10 135534747 820012 0.006050197592503714 0.20741001312120583 chr11 135006516 835350 0.006187479128785161 0.12811247338386364 chr12 133851895 522651 0.003904696306316769 0.10060881720052137 chr13 115169878 4882314 0.042392282468164115 0.3224198640755197 chr14 107349540 1811090 0.016870961906310915 0.2208148814788844 chr15 102531392 807775 0.007878318866479448 0.13294163679661608 chr16 90354753 1250760 0.013842769289624421 0.18381054464194485 chr17 81195210 408568 0.005031922449612483 0.11754897678265971 chr18 78077248 704427 0.009022180187498412 0.37882607401252394 chr19 59128983 534288 0.009035974794289968 0.17247552777211939 chr20 63025520 937968 0.014882352418512374 0.2130106066344613 chr21 48129895 1139950 0.02368486363828552 0.25381221608315063 chr22 51304566 179178 0.0034924376906336173 0.08323922295439128 chrMT 16571 14007 0.8452718604791504 1.4930556722602548 chrX 155270560 3815617 0.024573988784480458 0.2486421369060939 chrY 59373566 202607 0.003412410836162342 0.13717665071611773