BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240182.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 = 1,594,671 number of mapped reads = 1,215,570 (76.23%) number of supplementary alignments = 11,233 (0.7%) number of secondary alignments = 0 number of mapped bases = 79,852,116 bp number of sequenced bases = 79,814,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,178 duplication rate = 7.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7903 >>>>>>> ACTG content number of A's = 23,254,831 bp (29.14%) number of C's = 15,189,121 bp (19.03%) number of T's = 24,711,567 bp (30.96%) number of G's = 16,608,871 bp (20.81%) number of N's = 50,529 bp (0.06%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 731,755 number of insertions = 5,816 mapped reads with insertion percentage = 0.48% number of deletions = 21,419 mapped reads with deletion percentage = 1.74% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.3178X There is a 1.43% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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 0.01% 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 6561906 0.026326538219537676 0.5025566529039328 chr2 243199373 8372583 0.03442682806587664 0.35198303366588674 chr3 198022430 5038143 0.025442284492721356 0.2662933700845937 chr4 191154276 5327215 0.027868667714239362 0.2741420533542255 chr5 180915260 4233250 0.02339907645159397 0.2464491987393643 chr6 171115067 4127820 0.024123065679540655 0.27157847918232714 chr7 159138663 4809328 0.030220990357321276 0.38785052269112824 chr8 146364022 4442944 0.03035543803244215 0.38530505180925223 chr9 141213431 2881536 0.02040553777069548 0.27296634256085894 chr10 135534747 3925833 0.028965509486655848 0.32218029950874877 chr11 135006516 3443865 0.025508879882508783 0.30167774954679916 chr12 133851895 3955441 0.029550877856454702 0.28014039476550245 chr13 115169878 2105496 0.018281655208491236 0.2205236902812989 chr14 107349540 2602390 0.024242209142209644 0.26516248986842234 chr15 102531392 2233273 0.021781358435082984 0.26171110892420446 chr16 90354753 2354799 0.026061705907159085 0.26722736441871126 chr17 81195210 1909705 0.023519921926428912 0.25753245674525216 chr18 78077248 1885919 0.024154527065298203 0.4004876277146099 chr19 59128983 1453562 0.02458290209388516 0.3456972292382707 chr20 63025520 1535890 0.024369334834524175 0.2520218853957809 chr21 48129895 1281121 0.02661798867419096 0.2703638945157036 chr22 51304566 732431 0.014276136747750677 0.18844078144932305 chrMT 16571 15277 0.9219117735803513 1.5953648903550828 chrX 155270560 4405255 0.02837147621545256 0.2872368936112751 chrY 59373566 217134 0.003657082008515372 0.0976692233010879