BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082691.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 = 3,631,486 number of mapped reads = 3,374,909 (92.93%) number of supplementary alignments = 14,000 (0.39%) number of secondary alignments = 0 number of mapped bases = 223,338,424 bp number of sequenced bases = 223,255,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,300 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9398 >>>>>>> ACTG content number of A's = 61,388,312 bp (27.5%) number of C's = 38,158,520 bp (17.09%) number of T's = 74,594,712 bp (33.41%) number of G's = 49,054,174 bp (21.97%) number of N's = 59,319 bp (0.03%) GC percentage = 39.06% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,984,903 number of insertions = 19,806 mapped reads with insertion percentage = 0.58% number of deletions = 52,176 mapped reads with deletion percentage = 1.53% homopolymer indels = 49.38% >>>>>>> Coverage mean coverageData = 0.0721X std coverageData = 0.4975X There is a 5.89% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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% 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 21788296 0.08741521249810648 0.7057550016265667 chr2 243199373 20551244 0.08450368825580813 0.6785565487400703 chr3 198022430 19213771 0.09702825583950263 0.3676758775613504 chr4 191154276 11658804 0.060991594035803835 0.2962759446615496 chr5 180915260 14413404 0.07966936564665689 0.3367639673871586 chr6 171115067 14317083 0.0836693299486012 0.5682186912844787 chr7 159138663 10284145 0.0646237991832318 0.5719736380766975 chr8 146364022 20271881 0.1385031698568655 0.6385222544738545 chr9 141213431 6853298 0.04853148848143205 0.5770030837098976 chr10 135534747 9394855 0.06931694792627606 0.41148600241888955 chr11 135006516 9111593 0.06749002396299153 0.43381219703555546 chr12 133851895 7351794 0.0549248406232874 0.2823099016361534 chr13 115169878 5350155 0.046454464421678034 0.24666924428488543 chr14 107349540 4837963 0.04506738454584901 0.29476682792695996 chr15 102531392 4513007 0.04401585613896669 0.2424006610000919 chr16 90354753 7350268 0.08134899112612261 0.37105390940482585 chr17 81195210 5515593 0.06793002936995914 0.40801020104685426 chr18 78077248 6022097 0.07712998542161732 1.0658443322858702 chr19 59128983 2970862 0.05024375271260796 0.5290340649802959 chr20 63025520 4990868 0.07918804953929773 0.3462065558847885 chr21 48129895 3594219 0.07467747436390626 0.336386641396084 chr22 51304566 2821589 0.054996839852421715 0.2751125779564174 chrMT 16571 2941 0.1774787278981353 0.4585652596823897 chrX 155270560 9792866 0.06306968945046633 0.3589356401560917 chrY 59373566 365828 0.006161462493258363 0.11490482564132952