BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081223.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 = 2,411,709 number of mapped reads = 2,124,615 (88.1%) number of supplementary alignments = 25,510 (1.06%) number of secondary alignments = 0 number of mapped bases = 138,749,610 bp number of sequenced bases = 138,698,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,803 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3123 >>>>>>> ACTG content number of A's = 39,524,544 bp (28.5%) number of C's = 26,758,770 bp (19.29%) number of T's = 42,465,252 bp (30.62%) number of G's = 29,940,199 bp (21.59%) number of N's = 9,251 bp (0.01%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,214,569 number of insertions = 10,023 mapped reads with insertion percentage = 0.47% number of deletions = 31,517 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.41% >>>>>>> Coverage mean coverageData = 0.0448X std coverageData = 0.3529X There is a 3.68% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 15779525 0.06330786634228687 0.6425950756302261 chr2 243199373 9426866 0.03876188447245709 0.37869748377519863 chr3 198022430 8747416 0.04417386454655667 0.2493354876948796 chr4 191154276 6116688 0.031998698266106275 0.21569950869557047 chr5 180915260 8791251 0.048593197721408354 0.25873189738672236 chr6 171115067 8930702 0.0521912076859953 0.29085954620086474 chr7 159138663 9529567 0.059882160754360494 0.4947386960802416 chr8 146364022 6709292 0.045839762452004766 0.3842548443589038 chr9 141213431 3374894 0.023899242275332862 0.2405047280534675 chr10 135534747 4592174 0.033881894507834215 0.34029469431777715 chr11 135006516 7715045 0.05714572324790605 0.4309955631101794 chr12 133851895 4506844 0.033670378742116425 0.2176940753022203 chr13 115169878 4558144 0.03957757079503028 0.23431995653442667 chr14 107349540 5562875 0.05182020342145854 0.2732095617825335 chr15 102531392 2159926 0.021065997036302794 0.17313169596471917 chr16 90354753 5081504 0.0562394764113848 0.28784309666325686 chr17 81195210 2351358 0.0289593191519549 0.23303825875178802 chr18 78077248 3586009 0.04592898817335365 0.40636550660874965 chr19 59128983 3833632 0.06483507419703126 0.4992656765071799 chr20 63025520 3466595 0.055003036865066725 0.2775640720471346 chr21 48129895 2384240 0.04953761066796426 0.2710658657111055 chr22 51304566 1103908 0.02151675934652678 0.1700658299438098 chrMT 16571 49887 3.010500271558747 2.5937187319827633 chrX 155270560 10010045 0.06446840276740162 0.31896007254550107 chrY 59373566 381223 0.006420752966059004 0.11167362966829929