BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237803.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 = 2,488,734 number of mapped reads = 2,079,834 (83.57%) number of supplementary alignments = 10,623 (0.43%) number of secondary alignments = 0 number of mapped bases = 130,499,109 bp number of sequenced bases = 130,432,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,990 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0022 >>>>>>> ACTG content number of A's = 35,482,683 bp (27.2%) number of C's = 23,523,103 bp (18.03%) number of T's = 40,303,901 bp (30.9%) number of G's = 31,008,502 bp (23.77%) number of N's = 114,641 bp (0.09%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,124,805 number of insertions = 12,048 mapped reads with insertion percentage = 0.57% number of deletions = 40,335 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.4425X There is a 3.63% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12361798 0.0495958563730118 0.8131902381999834 chr2 243199373 12080281 0.049672336120702085 0.5026213449707476 chr3 198022430 9046322 0.045683319813821094 0.2701429964109782 chr4 191154276 6410638 0.03353646140774795 0.24585955169158324 chr5 180915260 6894703 0.038110124043709746 0.22498576119554342 chr6 171115067 8072146 0.04717378861792457 0.31671104384609333 chr7 159138663 7950875 0.04996193162688567 0.7122258926849594 chr8 146364022 7245485 0.04950318323447001 0.39015582713206876 chr9 141213431 4837405 0.034255983766869884 0.37507924907423335 chr10 135534747 6646160 0.04903657657618972 0.6664104053964764 chr11 135006516 6025746 0.044633001269360956 0.4243023269242901 chr12 133851895 6719469 0.050200776014415034 0.2682273063564643 chr13 115169878 4502972 0.039098521924283015 0.22777852519125835 chr14 107349540 3623812 0.03375712648605667 0.25313867870454276 chr15 102531392 2696948 0.026303631964735247 0.19943322439272673 chr16 90354753 3231433 0.03576384077990894 0.2843593988884777 chr17 81195210 3279251 0.04038724698168771 0.3161568160792438 chr18 78077248 2561567 0.03280811075718242 0.6696628955926209 chr19 59128983 2329850 0.039402842426699614 0.550943070799776 chr20 63025520 2714716 0.04307328206098101 0.255364237852037 chr21 48129895 1778670 0.03695561770911821 0.2558302626730737 chr22 51304566 1022630 0.019932533880122873 0.1640674117870917 chrMT 16571 66566 4.017017681491763 3.0087373401182327 chrX 155270560 7970634 0.05133383946061636 0.3043288688452635 chrY 59373566 429032 0.007225976624008064 0.16492336217447393