BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716918.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 = 740,826 number of mapped reads = 601,201 (81.15%) number of supplementary alignments = 2,100 (0.28%) number of secondary alignments = 0 number of mapped bases = 33,404,615 bp number of sequenced bases = 33,394,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,281 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.419 >>>>>>> ACTG content number of A's = 8,353,460 bp (25.01%) number of C's = 6,469,674 bp (19.37%) number of T's = 9,969,058 bp (29.85%) number of G's = 8,601,457 bp (25.76%) number of N's = 984 bp (0%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 179,918 number of insertions = 3,101 mapped reads with insertion percentage = 0.51% number of deletions = 5,798 mapped reads with deletion percentage = 0.95% homopolymer indels = 34.42% >>>>>>> Coverage mean coverageData = 0.0108X std coverageData = 0.1192X There is a 1.02% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 2683664 0.010766930045081011 0.12282391556787398 chr2 243199373 2765884 0.011372907610251117 0.14667924414612826 chr3 198022430 2150693 0.010860855510156097 0.11081061190504783 chr4 191154276 2104074 0.011007203417202134 0.12021620765341867 chr5 180915260 1945532 0.010753830273908348 0.10953542081684066 chr6 171115067 1872330 0.010941935346932366 0.11170923751174089 chr7 159138663 1838532 0.011553019017132248 0.13132093838295578 chr8 146364022 1649679 0.011271069060947232 0.11462667805954768 chr9 141213431 1401884 0.009927412641082278 0.10911752972003166 chr10 135534747 1654094 0.012204206202561473 0.14523641492045805 chr11 135006516 1488466 0.01102514192722372 0.12058560454975681 chr12 133851895 1536829 0.01148156326064715 0.11277970777130233 chr13 115169878 1012392 0.008790423482084439 0.09876368051774437 chr14 107349540 1002404 0.009337757758440325 0.102855049518733 chr15 102531392 995604 0.009710235866104306 0.10512022854792227 chr16 90354753 1086723 0.012027292023032812 0.12092638883000031 chr17 81195210 1012451 0.012469343942826184 0.12051669226222231 chr18 78077248 864512 0.011072521408541449 0.1325846116292306 chr19 59128983 802898 0.013578755447222896 0.13424871665824373 chr20 63025520 751824 0.011928882141710215 0.11796023963478988 chr21 48129895 456311 0.009480822677880349 0.1106754546992423 chr22 51304566 445042 0.00867451056890336 0.09981989394789317 chrMT 16571 2043 0.1232876712328767 0.36627511666357143 chrX 155270560 1763223 0.011355810141986994 0.11544925635031575 chrY 59373566 117527 0.0019794499121039825 0.06598371748496905