BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013275.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 = 2,768,976 number of mapped reads = 2,391,631 (86.37%) number of supplementary alignments = 18,565 (0.67%) number of secondary alignments = 0 number of mapped bases = 154,380,990 bp number of sequenced bases = 154,319,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,240 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1489 >>>>>>> ACTG content number of A's = 42,490,929 bp (27.53%) number of C's = 30,260,281 bp (19.61%) number of T's = 45,939,012 bp (29.77%) number of G's = 35,596,328 bp (23.07%) number of N's = 33,290 bp (0.02%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,242,461 number of insertions = 11,064 mapped reads with insertion percentage = 0.46% number of deletions = 35,244 mapped reads with deletion percentage = 1.46% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4112X There is a 4.4% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 11356568 0.045562847363979087 0.605338216278558 chr2 243199373 15526327 0.06384196969126232 0.5371092581577471 chr3 198022430 9534496 0.04814856579630904 0.23865688740825736 chr4 191154276 9292772 0.04861398967606668 0.2509477119959824 chr5 180915260 8164849 0.045130792173087 0.2364836954932693 chr6 171115067 8069532 0.04715851234771746 0.29673290174675576 chr7 159138663 9639374 0.06057216906491165 0.7844990331922632 chr8 146364022 8480112 0.05793850076079489 0.3735541867233241 chr9 141213431 5606504 0.03970234247760753 0.3372738046920682 chr10 135534747 7228830 0.05333562175019222 0.41723326740335503 chr11 135006516 6464370 0.04788191112197873 0.31426463273153893 chr12 133851895 7762972 0.057996728398951695 0.2676490863760837 chr13 115169878 3789771 0.03290592180708918 0.20697936777535159 chr14 107349540 5163124 0.04809637749728597 0.2757771291509884 chr15 102531392 4347275 0.04239945362294506 0.2306178980046414 chr16 90354753 5273120 0.05836018388540114 0.29786192012758095 chr17 81195210 4360797 0.05370756476890694 0.2802223291902197 chr18 78077248 3721713 0.04766706172840518 0.6249558192093347 chr19 59128983 3487450 0.058980381922009384 0.5019536533819375 chr20 63025520 3658736 0.058051659073975116 0.26929127581191104 chr21 48129895 2527629 0.05251681932819509 0.2722349931596931 chr22 51304566 1689953 0.032939621787269384 0.1981875930432897 chrMT 16571 576741 34.80423631645646 25.11738161441825 chrX 155270560 8294956 0.053422593439477514 0.28324953866403835 chrY 59373566 363019 0.006114151876948068 0.1180048142856035