BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,073,614 number of mapped reads = 8,796,890 (87.33%) number of secondary alignments = 0 number of mapped bases = 349,042,737 bp number of sequenced bases = 349,006,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 389,959 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2263 >>>>>>> ACTG content number of A's = 104,785,546 bp (30.02%) number of C's = 70,000,855 bp (20.06%) number of T's = 106,033,143 bp (30.38%) number of G's = 68,102,673 bp (19.51%) number of N's = 84,316 bp (0.02%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,459,942 number of insertions = 9,033 mapped reads with insertion percentage = 0.1% number of deletions = 28,512 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.79% >>>>>>> Coverage mean coverageData = 0.1128X std coverageData = 1.3672X There is a 9.19% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 28133529 0.11287245298377813 3.235588220797 chr2 243199373 30942353 0.1272303979171854 0.8082534596341525 chr3 198022430 24917474 0.1258315737262693 0.4286944414827692 chr4 191154276 25035238 0.13096875740305175 0.46001266915752154 chr5 180915260 22995421 0.1271060329570872 0.4453000527813645 chr6 171115067 21624518 0.12637413162454011 0.5534882041534831 chr7 159138663 19918210 0.12516260740483914 1.1866585489024453 chr8 146364022 19179991 0.13104307150018055 3.2710435898078383 chr9 141213431 14973044 0.10603130236245022 0.7887198608497874 chr10 135534747 16379680 0.12085225643280981 0.8808403617412246 chr11 135006516 16299199 0.12072898022196203 0.7930652038848924 chr12 133851895 16192481 0.12097311733987778 0.4714209940837654 chr13 115169878 12264953 0.10649445161346789 0.3718887551716326 chr14 107349540 10942813 0.10193628216758079 0.48789031822839085 chr15 102531392 9719033 0.09479080319128019 0.3573486687762215 chr16 90354753 8628123 0.09549163395975417 0.4748444319634183 chr17 81195210 7795838 0.09601352099464981 0.43207183688299183 chr18 78077248 9803884 0.12556646463768806 1.6632220548759784 chr19 59128983 5667234 0.09584528115425223 2.5381766441402074 chr20 63025520 6636485 0.10529837754611147 0.4146158975704991 chr21 48129895 4530483 0.0941303320940135 0.4469714771208853 chr22 51304566 3054100 0.05952881464780347 0.27868756592624944 chrMT 16571 4149 0.25037716492667916 0.5980167653660213 chrX 155270560 12429489 0.08005051955760319 0.499425637213996 chrY 59373566 975015 0.016421701873187134 0.26363028848258924