BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236097.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 = 3,646,204 number of mapped reads = 3,177,624 (87.15%) number of supplementary alignments = 20,256 (0.56%) number of secondary alignments = 0 number of mapped bases = 205,674,135 bp number of sequenced bases = 205,566,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 182,298 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0787 >>>>>>> ACTG content number of A's = 57,896,395 bp (28.16%) number of C's = 36,947,893 bp (17.97%) number of T's = 65,604,020 bp (31.91%) number of G's = 45,041,584 bp (21.91%) number of N's = 76,301 bp (0.04%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,859,245 number of insertions = 15,872 mapped reads with insertion percentage = 0.5% number of deletions = 62,990 mapped reads with deletion percentage = 1.96% homopolymer indels = 44.84% >>>>>>> Coverage mean coverageData = 0.0664X std coverageData = 0.6888X There is a 5.35% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.18% 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 0.01% 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 18186726 0.07296561961223759 1.107739897069114 chr2 243199373 12690903 0.05218312384382669 0.7529566339060721 chr3 198022430 19389662 0.09791649360125518 0.3723724333413912 chr4 191154276 9968799 0.05215054148200169 0.324462553892158 chr5 180915260 8870784 0.04903281237856884 0.2686427441195989 chr6 171115067 21431951 0.12524876608323451 0.5753937717883898 chr7 159138663 12870135 0.08087371577326875 0.8241061596262917 chr8 146364022 14306482 0.09774589277138065 1.7233114239296057 chr9 141213431 8346201 0.05910345029432788 0.5479136758754733 chr10 135534747 9950232 0.07341462038513268 0.5426686607452166 chr11 135006516 5845285 0.04329631763847606 0.44691668477810714 chr12 133851895 5596628 0.041812093881823637 0.27662018939207994 chr13 115169878 8166782 0.07091074629774288 0.3262892105655504 chr14 107349540 7337651 0.06835288721311708 0.34357915869541344 chr15 102531392 5384584 0.05251644296412166 0.2829587151928033 chr16 90354753 4426798 0.04899352666040712 0.34016695424871374 chr17 81195210 4378966 0.05393133412672989 0.32206837471022737 chr18 78077248 5962307 0.07636420535723801 1.23598911820301 chr19 59128983 3777871 0.06389203413155271 0.773182092137562 chr20 63025520 2636734 0.04183597374523844 0.2563783993868889 chr21 48129895 3007985 0.06249722755472456 0.3418775322210637 chr22 51304566 2303321 0.04489504891241064 0.24606280151500998 chrMT 16571 80812 4.876712328767123 3.8063505864919023 chrX 155270560 10262292 0.0660929670119049 0.3699035970692915 chrY 59373566 494244 0.00832431051892689 0.2036036892251938