BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081041.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 = 1,996,188 number of mapped reads = 1,645,814 (82.45%) number of supplementary alignments = 8,649 (0.43%) number of secondary alignments = 0 number of mapped bases = 105,846,465 bp number of sequenced bases = 105,807,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,020 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6509 >>>>>>> ACTG content number of A's = 30,846,007 bp (29.15%) number of C's = 20,053,687 bp (18.95%) number of T's = 31,687,319 bp (29.95%) number of G's = 23,218,781 bp (21.94%) number of N's = 1,408 bp (0%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 832,646 number of insertions = 7,097 mapped reads with insertion percentage = 0.43% number of deletions = 22,962 mapped reads with deletion percentage = 1.38% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.2848X There is a 3.05% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8469201 0.033978655563710713 0.48304847246736254 chr2 243199373 8939413 0.03675754953529424 0.2956046171163717 chr3 198022430 7296646 0.036847573277431246 0.2084339907415173 chr4 191154276 7045957 0.0368600543364251 0.21507192017299015 chr5 180915260 6527827 0.03608223540678658 0.20790741573115376 chr6 171115067 6375344 0.037257642542956194 0.26560058094631844 chr7 159138663 5617072 0.03529671479017013 0.3809421463411854 chr8 146364022 5165082 0.03528928714462356 0.30193411573268936 chr9 141213431 4580123 0.03243404658867045 0.27130256359166527 chr10 135534747 4848404 0.035772406023674506 0.2535663670483507 chr11 135006516 4926338 0.036489631359718964 0.2760651726278158 chr12 133851895 5023616 0.03753115336917718 0.21262521295637005 chr13 115169878 3451491 0.029968695460457117 0.1876570075779497 chr14 107349540 3204291 0.02984913582303194 0.20028935365411504 chr15 102531392 3209293 0.03130058938437118 0.2001814914531725 chr16 90354753 3054838 0.03380937801910653 0.21860360096475817 chr17 81195210 2838225 0.034955571886568185 0.22964683872018365 chr18 78077248 2820781 0.03612807920689008 0.49978408196076207 chr19 59128983 2046811 0.03461603592945273 0.34289908111608614 chr20 63025520 2157425 0.034230975008218895 0.20541815237111552 chr21 48129895 1478667 0.030722423142622687 0.22611748892235387 chr22 51304566 1153898 0.022491136558878598 0.1629066166758157 chrMT 16571 15243 0.9198599963792167 1.0800234430651403 chrX 155270560 5369670 0.03458266654026365 0.22402808123501747 chrY 59373566 230809 0.0038874033606133744 0.09124938775076204