BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084258.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 = 2,983,629 number of mapped reads = 2,279,207 (76.39%) number of supplementary alignments = 15,762 (0.53%) number of secondary alignments = 0 number of mapped bases = 146,272,459 bp number of sequenced bases = 146,222,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,171 duplication rate = 3.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7822 >>>>>>> ACTG content number of A's = 41,680,043 bp (28.5%) number of C's = 27,872,282 bp (19.06%) number of T's = 44,797,917 bp (30.64%) number of G's = 31,870,325 bp (21.8%) number of N's = 1,666 bp (0%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,224,040 number of insertions = 11,044 mapped reads with insertion percentage = 0.48% number of deletions = 31,782 mapped reads with deletion percentage = 1.38% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.3286X There is a 4.04% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11925872 0.04784690987790959 0.5062289235775965 chr2 243199373 12822825 0.05272556767652522 0.42117920484705906 chr3 198022430 10444604 0.05274455020070201 0.26107475316880074 chr4 191154276 9738479 0.050945650831268875 0.2659718642905326 chr5 180915260 9037893 0.04995649897084414 0.25328848617829086 chr6 171115067 9119689 0.05329565163306163 0.30117902744020086 chr7 159138663 7719149 0.048505805280015454 0.3820400385176709 chr8 146364022 7307558 0.0499272833592944 0.33811070740726734 chr9 141213431 6107119 0.043247437278115565 0.30700838700309807 chr10 135534747 6634368 0.04894957305671586 0.34537903949932736 chr11 135006516 6404879 0.047441258316746726 0.28551997298976955 chr12 133851895 6425668 0.04800580522225703 0.2522069563292728 chr13 115169878 4720661 0.0409886776123875 0.23037271539039386 chr14 107349540 4351052 0.04053163152818354 0.23786212930386702 chr15 102531392 4064157 0.03963817247307049 0.23200288638420538 chr16 90354753 3831441 0.04240442115978116 0.2549324461972211 chr17 81195210 3555046 0.043783937500746654 0.2596483044991675 chr18 78077248 3805262 0.04873714298946602 0.5402684104674069 chr19 59128983 2605459 0.04406399142701305 0.3939678856781036 chr20 63025520 2905727 0.04610397502472015 0.2492466112995017 chr21 48129895 1855269 0.03854712336272498 0.23426048788345294 chr22 51304566 1491448 0.029070472986751316 0.1932086472710201 chrMT 16571 29547 1.7830547341741596 1.9198252324931586 chrX 155270560 9016031 0.05806658390360671 0.29396610686708435 chrY 59373566 353256 0.005949718431936529 0.12081643828766661