BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068065.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 = 3,441,964 number of mapped reads = 3,228,609 (93.8%) number of supplementary alignments = 26,493 (0.77%) number of secondary alignments = 0 number of mapped bases = 207,265,437 bp number of sequenced bases = 207,186,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 469,571 duplication rate = 11.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3377 >>>>>>> ACTG content number of A's = 54,433,187 bp (26.27%) number of C's = 36,566,574 bp (17.65%) number of T's = 68,447,425 bp (33.04%) number of G's = 47,716,062 bp (23.03%) number of N's = 23,629 bp (0.01%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,120,335 number of insertions = 13,241 mapped reads with insertion percentage = 0.41% number of deletions = 45,530 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 0.8277X There is a 4.69% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.13% 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 22321924 0.0895561419684487 1.7340106435996991 chr2 243199373 16501730 0.06785268315638297 1.3200562928212016 chr3 198022430 16576497 0.08371019889009543 0.39398916389435235 chr4 191154276 9691998 0.0507024912170942 0.32610315503604603 chr5 180915260 7125213 0.03938425647455057 0.2744591033316547 chr6 171115067 18198896 0.10635472561863883 0.6212146179832828 chr7 159138663 14915867 0.09372874396965368 1.345399211945534 chr8 146364022 8476563 0.05791425299859552 1.0091000650677187 chr9 141213431 5759042 0.04078253717948401 0.4684877039680702 chr10 135534747 11998403 0.08852639832647491 0.5423932866791117 chr11 135006516 9487777 0.0702764376202405 0.4519704755490865 chr12 133851895 10263665 0.07667926554196337 0.38785726762372347 chr13 115169878 3939060 0.03420217220339506 0.30897891936008837 chr14 107349540 5825669 0.05426822508973955 0.3464822673714636 chr15 102531392 4178013 0.04074862262671709 0.31619503326995607 chr16 90354753 5034915 0.055723853287496676 0.340996867061849 chr17 81195210 6463670 0.07960654329239372 0.39974494950223965 chr18 78077248 4027164 0.05157922574320242 1.020590137137339 chr19 59128983 4931476 0.08340200946801335 1.0779802181239413 chr20 63025520 3081129 0.04888700640629383 0.306770695077806 chr21 48129895 3782762 0.07859485253396044 0.3882677503597056 chr22 51304566 2780064 0.05418745770113327 0.3062246547659059 chrMT 16571 231857 13.991732544807194 8.469108774239123 chrX 155270560 11094231 0.07145096275816872 0.40457787386413774 chrY 59373566 577852 0.009732479265267645 0.26054552152396443