BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238543.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 = 2,876,297 number of mapped reads = 2,549,597 (88.64%) number of supplementary alignments = 24,300 (0.84%) number of secondary alignments = 0 number of mapped bases = 156,552,429 bp number of sequenced bases = 156,457,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 643,936 duplication rate = 18.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3219 >>>>>>> ACTG content number of A's = 39,654,641 bp (25.35%) number of C's = 27,668,977 bp (17.68%) number of T's = 51,986,554 bp (33.23%) number of G's = 37,136,464 bp (23.74%) number of N's = 10,693 bp (0.01%) GC percentage = 41.42% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,017,176 number of insertions = 10,025 mapped reads with insertion percentage = 0.39% number of deletions = 55,635 mapped reads with deletion percentage = 2.16% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.6689X There is a 2.52% of reference with a coverageData >= 1X There is a 1.14% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 5208801 0.020897845626631356 0.4472645228809485 chr2 243199373 8466654 0.03481363416179531 1.3794358717642619 chr3 198022430 10120953 0.05111013434185208 0.40053699251254465 chr4 191154276 6598850 0.03452106925403019 0.32410055578106367 chr5 180915260 13146507 0.0726666562013619 0.47771529790323974 chr6 171115067 16044691 0.09376550692640058 0.9646764824074611 chr7 159138663 1510734 0.009493192738461049 0.3319279400986615 chr8 146364022 11986342 0.08189404633879219 0.7874241727556048 chr9 141213431 5123585 0.03628256153623234 0.5439574967758831 chr10 135534747 20128350 0.14851062510191576 0.7901772430287438 chr11 135006516 2038779 0.015101337775430039 0.3117840819325164 chr12 133851895 4850752 0.03623969612085059 0.3457654838728164 chr13 115169878 719887 0.006250653491184561 0.2889560801290141 chr14 107349540 7740477 0.07210535788043433 0.5016750269527435 chr15 102531392 4241679 0.04136956416235917 0.42938644499042594 chr16 90354753 2585526 0.028615273841764582 0.3486520068003553 chr17 81195210 1214333 0.014955722141737179 0.22581439626609964 chr18 78077248 14246659 0.18246876478023405 1.5399987686285805 chr19 59128983 1091756 0.01846397391952437 0.5366430903921259 chr20 63025520 2804516 0.04449810172133447 0.39491635904290706 chr21 48129895 4633829 0.09627756304060085 0.5605156975818535 chr22 51304566 1314703 0.025625457975806676 0.27889443778764145 chrMT 16571 20845 1.2579204634602619 1.7738732236407757 chrX 155270560 10357010 0.06670298606509824 0.5449040808318523 chrY 59373566 356211 0.005999488055004141 0.24467251754474154