BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068176.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 = 3,271,180 number of mapped reads = 3,083,221 (94.25%) number of supplementary alignments = 22,758 (0.7%) number of secondary alignments = 0 number of mapped bases = 196,976,706 bp number of sequenced bases = 196,893,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,146 duplication rate = 9.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6704 >>>>>>> ACTG content number of A's = 50,957,095 bp (25.88%) number of C's = 35,530,406 bp (18.05%) number of T's = 63,977,434 bp (32.49%) number of G's = 46,406,426 bp (23.57%) number of N's = 21,914 bp (0.01%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,090,741 number of insertions = 12,271 mapped reads with insertion percentage = 0.39% number of deletions = 47,841 mapped reads with deletion percentage = 1.54% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.0636X std coverageData = 0.6857X There is a 4.85% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% 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 26083446 0.1046474664550585 1.455431919391285 chr2 243199373 6468749 0.026598543080947827 0.9002488984625889 chr3 198022430 10671404 0.05388987500052393 0.2921174535080901 chr4 191154276 14268700 0.07464494281048675 0.355816309220942 chr5 180915260 7587956 0.04194204513206901 0.2592338419803032 chr6 171115067 14547625 0.085016622177403 0.4635915624356845 chr7 159138663 17272301 0.1085361701197653 1.2052383947774057 chr8 146364022 9634998 0.0658290054368689 0.7318447783257922 chr9 141213431 6126553 0.043385058748413245 0.43578369218648 chr10 135534747 5685827 0.04195106513903774 0.450418529348142 chr11 135006516 12043985 0.08921039781516917 0.5218373781448209 chr12 133851895 8470557 0.06328305624660749 0.33356148883706216 chr13 115169878 3894411 0.0338144927096302 0.2557512521379645 chr14 107349540 5029992 0.04685620450725732 0.3131008076145396 chr15 102531392 4462140 0.04351974466512656 0.2900758762439333 chr16 90354753 6029732 0.06673397690545399 0.34756900511815686 chr17 81195210 5079934 0.06256445423319923 0.3348941955120899 chr18 78077248 4239655 0.054300774023182785 0.890840025239513 chr19 59128983 3435705 0.058105261171158655 0.9277083348936733 chr20 63025520 4425736 0.07022133256496733 0.3486447947215694 chr21 48129895 2710040 0.05630679227536233 0.31123462437762583 chr22 51304566 2261422 0.0440783769616139 0.259487624237251 chrMT 16571 414355 25.004827711061495 12.88090811642208 chrX 155270560 15560209 0.10021351761724824 0.4512345217841347 chrY 59373566 571274 0.009621689221092094 0.22376047525462214