BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008706.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 = 2,937,900 number of mapped reads = 502,573 (17.11%) number of supplementary alignments = 2,253 (0.08%) number of secondary alignments = 0 number of mapped bases = 28,540,392 bp number of sequenced bases = 28,523,896 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,596 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.771 >>>>>>> ACTG content number of A's = 7,745,180 bp (27.15%) number of C's = 4,279,709 bp (15%) number of T's = 9,594,243 bp (33.64%) number of G's = 6,899,085 bp (24.19%) number of N's = 5,679 bp (0.02%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 310,105 number of insertions = 2,846 mapped reads with insertion percentage = 0.56% number of deletions = 10,851 mapped reads with deletion percentage = 2.14% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.286X There is a 0.8% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 2373459 0.009522379484863952 0.15133127958514164 chr2 243199373 2484125 0.010214356103623671 0.44663933000788064 chr3 198022430 2145006 0.010832136541299893 0.15945967917536757 chr4 191154276 1693909 0.008861475847916685 0.14727358369497273 chr5 180915260 1583832 0.008754551716643471 0.13014290377684892 chr6 171115067 1692308 0.009889883045775273 0.3723029156102451 chr7 159138663 1605851 0.010090891614440671 0.28841867724149683 chr8 146364022 1815111 0.012401346828252642 0.18698260853512208 chr9 141213431 1074127 0.007606408203480305 0.12814460112453638 chr10 135534747 1365248 0.010073047909994623 0.2123417241286397 chr11 135006516 1208841 0.00895394560067012 0.12895827640043736 chr12 133851895 1390853 0.010390984752214378 0.1553737737985645 chr13 115169878 904660 0.007855005281849825 0.1991632095338875 chr14 107349540 904809 0.008428624845527982 0.12211732124791914 chr15 102531392 791096 0.007715646735782149 0.17241946974788888 chr16 90354753 737370 0.008160832446744667 0.19330306235683592 chr17 81195210 792872 0.009765009536892633 1.0193868556103118 chr18 78077248 670579 0.008588660809356396 0.4681644961718516 chr19 59128983 495633 0.008382234478817266 0.17782648005223287 chr20 63025520 579131 0.009188833348776813 0.12102246952997728 chr21 48129895 332791 0.006914434365585049 0.1083951216829363 chr22 51304566 296309 0.005775489846264366 0.09780447761385744 chrMT 16571 11573 0.6983887514332268 1.1053086861988115 chrX 155270560 1483862 0.009556621680246404 0.25275592784914264 chrY 59373566 107037 0.001802771960841968 0.22254214667972244