BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013342.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,063,716 number of mapped reads = 1,868,439 (90.54%) number of supplementary alignments = 8,751 (0.42%) number of secondary alignments = 0 number of mapped bases = 124,767,738 bp number of sequenced bases = 124,718,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,734 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5111 >>>>>>> ACTG content number of A's = 33,668,708 bp (27%) number of C's = 24,045,555 bp (19.28%) number of T's = 38,330,166 bp (30.73%) number of G's = 28,641,212 bp (22.96%) number of N's = 32,626 bp (0.03%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 940,233 number of insertions = 8,361 mapped reads with insertion percentage = 0.44% number of deletions = 28,659 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.17% >>>>>>> Coverage mean coverageData = 0.0403X std coverageData = 0.3058X There is a 3.41% of reference with a coverageData >= 1X There is a 0.47% 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 9058443 0.036342709854271536 0.33415335704076754 chr2 243199373 12630742 0.05193575067317299 0.44467176537432795 chr3 198022430 7916603 0.03997831457779808 0.22781778667948951 chr4 191154276 7385050 0.038633977510395844 0.2283384178073253 chr5 180915260 6556539 0.03624093954263449 0.21825035783575275 chr6 171115067 6509645 0.03804250037198653 0.2653760950447892 chr7 159138663 7699826 0.048384382869925205 0.5120889687721566 chr8 146364022 6935174 0.04738305155347535 0.31113655185923345 chr9 141213431 4648423 0.0329177116304185 0.2627197923870668 chr10 135534747 5784782 0.04268117311644076 0.29000456229678895 chr11 135006516 5226489 0.038712864792392686 0.2503156155978556 chr12 133851895 6161188 0.04602988997652965 0.2483475152965769 chr13 115169878 3141521 0.027277279915152816 0.1956273424479668 chr14 107349540 4227873 0.03938417435230743 0.23411873778181416 chr15 102531392 3690855 0.035997316802253106 0.22227461446374305 chr16 90354753 4250816 0.047045848268767884 0.2766686384192566 chr17 81195210 3493251 0.04302287043780045 0.24746944491773837 chr18 78077248 2976457 0.03812195071219723 0.4131195303490714 chr19 59128983 2795585 0.04727943654975429 0.32389885611189745 chr20 63025520 3019841 0.04791457492139692 0.25441243783269546 chr21 48129895 2078227 0.043179545685690775 0.2516116988624018 chr22 51304566 1454299 0.02834638538799841 0.193814243218889 chrMT 16571 347910 20.99511194255024 18.53670445611533 chrX 155270560 6527138 0.042037189793094065 0.24578092519361303 chrY 59373566 251061 0.004228497914374892 0.0870903966855022