BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080814.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,987,234 number of mapped reads = 2,454,272 (82.16%) number of supplementary alignments = 26,288 (0.88%) number of secondary alignments = 0 number of mapped bases = 167,468,115 bp number of sequenced bases = 167,406,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 183,069 duplication rate = 6.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9678 >>>>>>> ACTG content number of A's = 49,338,110 bp (29.47%) number of C's = 31,172,759 bp (18.62%) number of T's = 51,713,652 bp (30.89%) number of G's = 35,159,210 bp (21%) number of N's = 22,852 bp (0.01%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,357,776 number of insertions = 13,427 mapped reads with insertion percentage = 0.54% number of deletions = 34,821 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.4343X There is a 3.41% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% 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 12865403 0.05161633278337951 0.4772481933082915 chr2 243199373 14512515 0.05967332407555179 0.47075375943725445 chr3 198022430 11416559 0.057652857810097574 0.3517858665712087 chr4 191154276 11549079 0.06041758124207486 0.38707136981618256 chr5 180915260 10237686 0.056588294431326576 0.3478718880095778 chr6 171115067 10893040 0.063659151651444 0.41848858265775973 chr7 159138663 9457161 0.059427173898023766 0.4112303786907853 chr8 146364022 7988202 0.05457763383955109 0.9162624190124791 chr9 141213431 7992018 0.056595310682593644 0.4102184129961964 chr10 135534747 7824449 0.057730206999980604 0.4324687871864207 chr11 135006516 6563696 0.048617623759730236 0.3571009382406562 chr12 133851895 7686866 0.057428144741619086 0.3538553588281125 chr13 115169878 5388415 0.046786669340745504 0.3178035501915511 chr14 107349540 5122814 0.047720875189590936 0.33198259395639135 chr15 102531392 4836582 0.04717171888195958 0.3160594460903119 chr16 90354753 4921250 0.05446586744584427 0.3562444309821178 chr17 81195210 4075851 0.05019817055710552 0.3363296628010322 chr18 78077248 4136301 0.05297703371922125 0.6091704252591073 chr19 59128983 2607787 0.04410336298190686 0.4432315808847566 chr20 63025520 3578989 0.05678634622927348 0.3522322034590457 chr21 48129895 2332303 0.048458510038303634 0.3428952888086296 chr22 51304566 1628567 0.03174312009578251 0.25482938157817503 chrMT 16571 12511 0.7549936636292318 1.417479999460521 chrX 155270560 9395080 0.06050780006203365 0.37001090071707127 chrY 59373566 444991 0.007494766273597244 0.19205349122059978