BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716960.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 735,262 number of mapped reads = 593,795 (80.76%) number of supplementary alignments = 2,336 (0.32%) number of secondary alignments = 0 number of mapped bases = 33,561,711 bp number of sequenced bases = 33,551,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,167 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9291 >>>>>>> ACTG content number of A's = 8,588,142 bp (25.6%) number of C's = 6,278,707 bp (18.71%) number of T's = 10,811,228 bp (32.22%) number of G's = 7,872,535 bp (23.46%) number of N's = 508 bp (0%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 171,379 number of insertions = 2,744 mapped reads with insertion percentage = 0.46% number of deletions = 6,802 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.26% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1335X There is a 1.03% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2695872 0.010815908859861978 0.1503742763306241 chr2 243199373 3235807 0.01330516176947545 0.1662009493561111 chr3 198022430 2343362 0.011833821047443968 0.11437625135048028 chr4 191154276 1886578 0.009869399939554583 0.10417633844432786 chr5 180915260 1781638 0.009847914432425435 0.10246798575994358 chr6 171115067 1857818 0.010857126917993726 0.11395248258778669 chr7 159138663 2198009 0.013811910685714383 0.26777245199419564 chr8 146364022 2439714 0.016668809497459698 0.14796548920246008 chr9 141213431 1340239 0.009490874844617294 0.10888126771168012 chr10 135534747 1530389 0.011291488226262745 0.14536200344073916 chr11 135006516 1074835 0.007961356472601664 0.1027510577965531 chr12 133851895 1814965 0.013559501716430685 0.1221316478289176 chr13 115169878 1135167 0.009856457432385229 0.10228448893158187 chr14 107349540 1060898 0.0098826506382794 0.10418617914870018 chr15 102531392 775903 0.007567467727347348 0.09054196667212257 chr16 90354753 981608 0.010863933190100138 0.11130597404475598 chr17 81195210 1326915 0.016342281767606735 0.13475380337709644 chr18 78077248 747464 0.009573390701475544 0.1308372489855514 chr19 59128983 639252 0.010811144849218867 0.14077027077011373 chr20 63025520 712413 0.011303564016607875 0.11056465607383947 chr21 48129895 247612 0.00514466113005233 0.07544420784600231 chr22 51304566 461173 0.008988927028444213 0.09824634506231757 chrMT 16571 15318 0.9243859754993664 1.0827537046868403 chrX 155270560 1188043 0.007651437593836205 0.09738762140081696 chrY 59373566 70719 0.0011910856087033747 0.041548826314642254