BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714217.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 169,812 number of mapped reads = 37,101 (21.85%) number of supplementary alignments = 1,292 (0.76%) number of secondary alignments = 0 number of mapped bases = 4,045,974 bp number of sequenced bases = 3,992,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,031 duplication rate = 46.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.7218 >>>>>>> ACTG content number of A's = 606,032 bp (15.18%) number of C's = 492,600 bp (12.34%) number of T's = 551,118 bp (13.8%) number of G's = 2,342,845 bp (58.68%) number of N's = 54 bp (0%) GC percentage = 71.02% >>>>>>> Mismatches and indels general error rate = 0.0356 number of mismatches = 124,404 number of insertions = 3,032 mapped reads with insertion percentage = 5.91% number of deletions = 6,881 mapped reads with deletion percentage = 18% homopolymer indels = 38.9% >>>>>>> Coverage mean coverageData = 0.0013X std coverageData = 2.3354X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 86688 3.477945196373252E-4 0.32500751084400675 chr2 243199373 1965761 0.00808291968746153 8.272792527629065 chr3 198022430 37005 1.8687276991803404E-4 0.04125052681271586 chr4 191154276 31805 1.663839316887685E-4 0.04392837567748913 chr5 180915260 43110 2.3828835665935534E-4 0.07434127548104061 chr6 171115067 57902 3.38380488726922E-4 0.11407297889118567 chr7 159138663 58364 3.667493423644008E-4 0.13894578612264097 chr8 146364022 90785 6.2026855206261E-4 0.2479058696725057 chr9 141213431 24597 1.7418314834372943E-4 0.06233060072150914 chr10 135534747 46679 3.4440614700819117E-4 0.41508314505349053 chr11 135006516 30202 2.2370772089252343E-4 0.052477752015530885 chr12 133851895 38736 2.893944833578934E-4 0.07014035687952698 chr13 115169878 19370 1.681863377505705E-4 0.04536051091187443 chr14 107349540 42321 3.942355039434729E-4 0.13748216110082004 chr15 102531392 18701 1.823929202092565E-4 0.04850606082901437 chr16 90354753 23690 2.6218875281525035E-4 0.059427173126683844 chr17 81195210 39714 4.891175230657079E-4 0.1350292814451491 chr18 78077248 12371 1.5844564603506516E-4 0.03109731719330814 chr19 59128983 20002 3.3827742310399623E-4 0.14713535850955925 chr20 63025520 53755 8.529084726314039E-4 0.31366776407883884 chr21 48129895 5343 1.1101208510843416E-4 0.024171938926326186 chr22 51304566 4177 8.141575547096529E-5 0.017949025963953456 chrMT 16571 1644 0.09920946231368052 0.4946943460719741 chrX 155270560 1289482 0.008304742380010737 1.017565403026571 chrY 59373566 3770 6.349627037729215E-5 0.013467480286236335