BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046442.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 8,593,304 number of mapped reads = 8,550,915 (99.51%) number of supplementary alignments = 45,827 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,279,792 number of mapped paired reads (second in pair) = 4,271,123 number of mapped paired reads (both in pair) = 8,521,270 number of mapped paired reads (singletons) = 29,645 number of mapped bases = 825,456,104 bp number of sequenced bases = 825,205,833 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,598,699 duplication rate = 39.79% >>>>>>> Insert size mean insert size = 22,073.7942 std insert size = 1,466,210.524 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 52.6047 >>>>>>> ACTG content number of A's = 241,171,385 bp (29.23%) number of C's = 172,000,363 bp (20.84%) number of T's = 241,002,867 bp (29.21%) number of G's = 170,959,697 bp (20.72%) number of N's = 71,521 bp (0.01%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 2,806,625 number of insertions = 72,120 mapped reads with insertion percentage = 0.83% number of deletions = 96,898 mapped reads with deletion percentage = 1.11% homopolymer indels = 47.88% >>>>>>> Coverage mean coverageData = 0.2666X std coverageData = 27.529X There is a 2.24% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 198296301 0.7955699376171264 54.319525253559384 chr2 243199373 62922602 0.2587284713106559 18.482278315187596 chr3 198022430 32597039 0.16461286229039812 11.306448727807158 chr4 191154276 23128693 0.12099490256759937 10.050234363126554 chr5 180915260 25498807 0.14094337315713446 9.799506560836214 chr6 171115067 63231724 0.3695275063066188 31.849965357067873 chr7 159138663 39962124 0.2511151171352998 18.269481580326126 chr8 146364022 74010783 0.5056624024721048 36.5435611593401 chr9 141213431 10095092 0.07148818585110364 6.488415242139371 chr10 135534747 25146895 0.18553836235072618 22.37458494060186 chr11 135006516 20060878 0.1485919242594187 13.495399378945116 chr12 133851895 11267933 0.08418209544213028 6.9433259134065315 chr13 115169878 6335069 0.05500630121358642 3.1558122014985597 chr14 107349540 49013502 0.45657859362974446 34.27626431101244 chr15 102531392 10934511 0.10664549448426487 5.632507022922149 chr16 90354753 108916951 1.2054368739185197 85.75118841781071 chr17 81195210 35899359 0.44213641420472954 40.38356033930146 chr18 78077248 4932930 0.06318012130755428 3.0286500956734224 chr19 59128983 3751612 0.06344793719858162 3.8762899913575777 chr20 63025520 3708771 0.05884554383684577 3.3899238317921188 chr21 48129895 1488606 0.030928926813573974 1.7642576699024337 chr22 51304566 765643 0.014923486537241149 1.1888485780816846 chrMT 16571 38151 2.3022750588377288 2.3162351592444432 chrX 155270560 13349980 0.08597882302994206 7.372784361175758 chrY 59373566 102148 0.0017204289194959251 0.09469605992500435