BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081202.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 9,098,886 number of mapped reads = 6,661,661 (73.21%) number of supplementary alignments = 75,683 (0.83%) number of secondary alignments = 0 number of mapped bases = 444,851,584 bp number of sequenced bases = 444,707,107 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 786,653 duplication rate = 8.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5393 >>>>>>> ACTG content number of A's = 122,614,008 bp (27.57%) number of C's = 85,473,665 bp (19.22%) number of T's = 138,061,185 bp (31.05%) number of G's = 98,302,741 bp (22.11%) number of N's = 255,508 bp (0.06%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 4,598,322 number of insertions = 32,595 mapped reads with insertion percentage = 0.49% number of deletions = 93,189 mapped reads with deletion percentage = 1.38% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.1437X std coverageData = 1.4531X There is a 8.85% of reference with a coverageData >= 1X There is a 3.09% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.1% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 35320808 0.14170800400934608 2.578984010308717 chr2 243199373 37593691 0.15457972007189344 1.0465466692809138 chr3 198022430 31306231 0.15809436840058977 0.6009236123919762 chr4 191154276 27977729 0.1463620358667781 0.5914408661276538 chr5 180915260 28080945 0.15521601107612482 0.590257924193942 chr6 171115067 26330960 0.15387867627109658 0.8257627260912732 chr7 159138663 24567311 0.15437675883955365 2.219035422947472 chr8 146364022 22678455 0.15494555759064887 1.8589627166401004 chr9 141213431 18062218 0.12790722434893603 0.9644734739834414 chr10 135534747 21540880 0.158932528202528 1.423265772902009 chr11 135006516 21020948 0.15570321065095852 1.0837439022025142 chr12 133851895 19813327 0.14802425471824662 0.6002708727327497 chr13 115169878 14213787 0.12341583795026682 0.5162558389869619 chr14 107349540 14297874 0.13318989536424655 3.9047374063316553 chr15 102531392 12350634 0.12045709864155556 0.5089628348576609 chr16 90354753 11701073 0.12950146629253692 0.6408527993001744 chr17 81195210 11239837 0.13842980392562565 0.7493637650160937 chr18 78077248 12104225 0.15502883759427585 1.8828886717106277 chr19 59128983 7841457 0.13261613175386425 1.8413030655971132 chr20 63025520 8993347 0.14269373739399532 0.6576956048351573 chr21 48129895 5957870 0.12378730516657059 0.5795825914485727 chr22 51304566 5003825 0.09753176744541607 0.4637027784695084 chrMT 16571 97745 5.898557721320379 4.83159154662416 chrX 155270560 25649532 0.16519250011077438 0.69360853105037 chrY 59373566 1106875 0.01864255551030908 0.3272974049915201