BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084905.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 = 2,182,586 number of mapped reads = 1,966,971 (90.12%) number of supplementary alignments = 13,313 (0.61%) number of secondary alignments = 0 number of mapped bases = 133,549,670 bp number of sequenced bases = 133,499,295 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,588 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.709 >>>>>>> ACTG content number of A's = 37,983,797 bp (28.45%) number of C's = 24,205,236 bp (18.13%) number of T's = 42,929,682 bp (32.16%) number of G's = 28,360,480 bp (21.24%) number of N's = 20,100 bp (0.02%) GC percentage = 39.38% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,104,543 number of insertions = 10,564 mapped reads with insertion percentage = 0.53% number of deletions = 29,083 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.74% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.3852X There is a 3.66% of reference with a coverageData >= 1X There is a 0.49% 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 11569344 0.04641651023208484 0.8093997270113001 chr2 243199373 12871270 0.05292476638087385 0.4458217645271208 chr3 198022430 7306486 0.036897264617952626 0.21833991200660913 chr4 191154276 5639313 0.029501369877804877 0.2061774861540407 chr5 180915260 7411467 0.04096651106158762 0.23840498221524145 chr6 171115067 7451955 0.043549379552882975 0.24372826541803866 chr7 159138663 7433456 0.04671055958287145 0.36551654701289754 chr8 146364022 9253015 0.06321919057403329 0.5315072807676089 chr9 141213431 9695838 0.06866087688217136 0.43561124236972776 chr10 135534747 5605716 0.04135999161897576 0.3058473738815655 chr11 135006516 4852797 0.035944909503479075 0.2647198403323704 chr12 133851895 5459124 0.040784809210209536 0.2312023877740507 chr13 115169878 3986737 0.03461614329399568 0.2096747552085222 chr14 107349540 3206111 0.029866089784828142 0.20792407626628195 chr15 102531392 4071689 0.03971163290165806 0.2258800285698925 chr16 90354753 2683201 0.029696290575881492 0.21320671269761515 chr17 81195210 4016248 0.04946410016058829 0.25523169017450764 chr18 78077248 4893447 0.06267442981596892 0.6633444559867766 chr19 59128983 2452480 0.04147678305239919 0.4411838336844102 chr20 63025520 2969819 0.04712089642417865 0.2532195400872669 chr21 48129895 1388725 0.02885368854430287 0.20661319449653862 chr22 51304566 1769544 0.034490965190115824 0.20821990677341248 chrMT 16571 94016 5.673526039466538 3.2332590104309498 chrX 155270560 7179055 0.04623577708485111 0.26091581606625797 chrY 59373566 288817 0.004864403798821853 0.115329803314523