BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236089.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 = 2,974,384 number of mapped reads = 2,591,464 (87.13%) number of supplementary alignments = 15,776 (0.53%) number of secondary alignments = 0 number of mapped bases = 172,719,432 bp number of sequenced bases = 172,623,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,698 duplication rate = 4.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1314 >>>>>>> ACTG content number of A's = 48,506,456 bp (28.1%) number of C's = 30,372,952 bp (17.59%) number of T's = 56,287,603 bp (32.61%) number of G's = 37,360,503 bp (21.64%) number of N's = 95,509 bp (0.06%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,447,166 number of insertions = 12,344 mapped reads with insertion percentage = 0.47% number of deletions = 55,624 mapped reads with deletion percentage = 2.12% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0558X std coverageData = 0.6284X There is a 4.43% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14499964 0.05817423419779564 1.2710200198396229 chr2 243199373 11232913 0.046188083716811226 0.4753870561503249 chr3 198022430 16411598 0.082877469991657 0.3483819738000464 chr4 191154276 9298911 0.04864610509680673 0.27623594498890025 chr5 180915260 9252557 0.05114304343370482 0.27526529606498734 chr6 171115067 16650047 0.09730321994380542 0.5408393018373866 chr7 159138663 11794367 0.07411377460171323 0.934221544393708 chr8 146364022 12393706 0.0846772713037361 1.452531814075595 chr9 141213431 6290711 0.044547540240701324 0.41765346963764727 chr10 135534747 7080944 0.05224449196042694 0.4756418228114077 chr11 135006516 5999669 0.044439847629280355 0.3443963704091706 chr12 133851895 4677994 0.03494903079257862 0.24028267119613714 chr13 115169878 5827950 0.05060307522423528 0.2727363712379911 chr14 107349540 4114491 0.038327979793858456 0.2492884661695315 chr15 102531392 4798678 0.04680203698004997 0.26412922263463395 chr16 90354753 6221249 0.06885358869831673 0.33100660745767124 chr17 81195210 4185526 0.0515489275783633 0.3120116974229228 chr18 78077248 4770013 0.06109350831627672 0.5918926661896721 chr19 59128983 4022645 0.0680316960635024 0.8302063072574634 chr20 63025520 2748976 0.043616871387971094 0.2565244489091866 chr21 48129895 2429084 0.05046933927447795 0.2873680668798433 chr22 51304566 785310 0.015306824737587684 0.14225070136431117 chrMT 16571 227322 13.71806167400881 8.607536050445109 chrX 155270560 6689808 0.043084844931325035 0.27797475318650416 chrY 59373566 314999 0.005305374448959323 0.12543934679201993