BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084828.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 = 1,625,936 number of mapped reads = 1,494,222 (91.9%) number of supplementary alignments = 13,952 (0.86%) number of secondary alignments = 0 number of mapped bases = 101,018,735 bp number of sequenced bases = 100,978,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,651 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8489 >>>>>>> ACTG content number of A's = 28,384,542 bp (28.11%) number of C's = 18,433,510 bp (18.25%) number of T's = 32,367,868 bp (32.05%) number of G's = 21,778,326 bp (21.57%) number of N's = 14,514 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 834,499 number of insertions = 8,592 mapped reads with insertion percentage = 0.57% number of deletions = 24,315 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.8% >>>>>>> Coverage mean coverageData = 0.0326X std coverageData = 0.3613X There is a 2.72% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% 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 7526714 0.030197373109052354 0.6349578996297363 chr2 243199373 8307964 0.034161124255859 0.48169047385230207 chr3 198022430 6997326 0.03533602733791318 0.2171447184156745 chr4 191154276 7001709 0.036628576386122796 0.2240591384344274 chr5 180915260 5984794 0.033080647812683134 0.235464846664997 chr6 171115067 5313976 0.03105498594112697 0.22230062952796845 chr7 159138663 5728243 0.0359952942422295 0.4055183227839794 chr8 146364022 5615025 0.03836342376543875 0.46273464868708614 chr9 141213431 7020271 0.04971390433817871 0.4267262668212378 chr10 135534747 3180272 0.02346462490537574 0.24328297302846277 chr11 135006516 4182709 0.030981534254242958 0.31464235692277837 chr12 133851895 4189440 0.03129907126081405 0.21635945844666085 chr13 115169878 3022050 0.02623993402163715 0.1853106792903903 chr14 107349540 2066956 0.019254446735402872 0.19152410085043614 chr15 102531392 1769297 0.01725614921915817 0.15684789847684885 chr16 90354753 1674668 0.018534365314462207 0.18115410735954868 chr17 81195210 2528577 0.03114194790554763 0.23056791652323994 chr18 78077248 4457504 0.05709094664811956 0.8003446820993493 chr19 59128983 2172948 0.0367492875701921 0.4040560528374953 chr20 63025520 1988074 0.03154395235453829 0.22122120729970682 chr21 48129895 1046084 0.021734599670329636 0.1894591277449017 chr22 51304566 724610 0.014123694175680192 0.13400662293582224 chrMT 16571 13663 0.8245127029147306 1.0768458866287856 chrX 155270560 8267951 0.05324867122267093 0.3050930026779348 chrY 59373566 237910 0.004007002038583972 0.12791048547086775