BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068120.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 = 1,593,841 number of mapped reads = 960,580 (60.27%) number of supplementary alignments = 8,887 (0.56%) number of secondary alignments = 0 number of mapped bases = 63,697,159 bp number of sequenced bases = 63,673,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,360 duplication rate = 11.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.534 >>>>>>> ACTG content number of A's = 17,705,222 bp (27.81%) number of C's = 11,519,940 bp (18.09%) number of T's = 20,500,520 bp (32.2%) number of G's = 13,884,614 bp (21.81%) number of N's = 63,079 bp (0.1%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 558,919 number of insertions = 5,255 mapped reads with insertion percentage = 0.54% number of deletions = 14,555 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 0.3679X There is a 0.78% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 5086381 0.02040669338994345 0.5018530882298576 chr2 243199373 5334555 0.021934904412767544 0.393429338326261 chr3 198022430 4397847 0.022208832605478075 0.3382099474262195 chr4 191154276 4200135 0.021972487813979112 0.3611980622748815 chr5 180915260 3965074 0.02191674710027225 0.3377226483138137 chr6 171115067 3878187 0.02266420525084445 0.3543746023256256 chr7 159138663 4106705 0.02580582821661635 0.45511486643648197 chr8 146364022 3283462 0.02243353219686734 0.4223260125772181 chr9 141213431 2589140 0.018334941525498378 0.32489453984621525 chr10 135534747 3057087 0.022555743583599266 0.37996719114336386 chr11 135006516 2790920 0.020672483689602065 0.3348107202582098 chr12 133851895 3014931 0.022524380398200563 0.347575760138507 chr13 115169878 2399060 0.020830620312022905 0.34132562507866776 chr14 107349540 1794770 0.016718935171962546 0.29192854282578223 chr15 102531392 1735158 0.0169231877784318 0.32712833894630144 chr16 90354753 1443569 0.01597668027491592 0.28161336705383055 chr17 81195210 1324157 0.016308314246616273 0.2869652164218235 chr18 78077248 1881636 0.024099671135949872 0.44026713145501606 chr19 59128983 1335890 0.022592812056314245 0.4056079184138441 chr20 63025520 1229505 0.01950805007241511 0.3208980229907097 chr21 48129895 803510 0.016694613607613314 0.29185489178172613 chr22 51304566 496044 0.009668613121101151 0.2094347171413116 chrMT 16571 17858 1.0776658017017682 2.1106685807927805 chrX 155270560 3334094 0.02147280205597249 0.33838765988662606 chrY 59373566 197484 0.0033261266469997775 0.13183401821807234