BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082480.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 = 1,693,385 number of mapped reads = 1,493,815 (88.21%) number of supplementary alignments = 11,637 (0.69%) number of secondary alignments = 0 number of mapped bases = 101,619,825 bp number of sequenced bases = 101,584,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,831 duplication rate = 2.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1399 >>>>>>> ACTG content number of A's = 29,111,247 bp (28.66%) number of C's = 19,120,701 bp (18.82%) number of T's = 30,866,300 bp (30.38%) number of G's = 22,484,206 bp (22.13%) number of N's = 2,022 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 850,703 number of insertions = 8,203 mapped reads with insertion percentage = 0.54% number of deletions = 21,750 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.2822X There is a 2.97% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% 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 8086960 0.03244509469045616 0.45538685749369573 chr2 243199373 8693866 0.035747896438861296 0.32570414715925317 chr3 198022430 6954985 0.03512220812561486 0.2014893919591961 chr4 191154276 6853543 0.03585346424581159 0.20711755727563663 chr5 180915260 6312307 0.03489095944698087 0.2016732322658076 chr6 171115067 6069305 0.03546914428055596 0.22596677957444272 chr7 159138663 5613020 0.035271252718768915 0.3390244182050206 chr8 146364022 5213793 0.035622094342283105 0.47519001858905163 chr9 141213431 4248536 0.030085920085037802 0.2576196882616687 chr10 135534747 4709799 0.03474975313894967 0.2602914974658798 chr11 135006516 4577133 0.033903052501554815 0.23808137720408978 chr12 133851895 4576823 0.03419318792610295 0.20092542481354758 chr13 115169878 3392679 0.029458041103421158 0.18417091864904805 chr14 107349540 3079213 0.028683988771633303 0.18958833684861057 chr15 102531392 2869408 0.027985653408470257 0.18044817412080558 chr16 90354753 2761435 0.030562144306896615 0.2034771871792176 chr17 81195210 2516531 0.03099358940016289 0.1984290752010342 chr18 78077248 2787093 0.03569660908130368 0.4304617950685284 chr19 59128983 1822137 0.030816308814240894 0.36165038788032877 chr20 63025520 1945388 0.03086667115162239 0.19105226760477068 chr21 48129895 1328659 0.027605690808176497 0.1846572060686752 chr22 51304566 1043737 0.02034393975772059 0.15277487894026723 chrMT 16571 22543 1.3603886307404502 1.3888353814758307 chrX 155270560 5904613 0.038027897883539545 0.22440245421881638 chrY 59373566 236319 0.003980205601934033 0.08892483115189026