mTCW overview for ex

Project: ex  Cluster: 971  Pairs: 989  Seqs: 707  Hits: 2.9k   PCC Stats KaKs Multi

Created: 13-Aug-21 v3.3.0

DATASETS: 3
           Type  #Seq  #annotated  #annoDB  Created    Remark  
      bar  NT     250         250        3  13-Aug-21  exBar   
      fly  NT     207         207        3  13-Aug-21  exFly   
      foo  NT     250         250        3  13-Aug-21  exFoo   
                           
CLUSTER SETS: 5
      Prefix  Method        Parameters                             
      BBa     BBH           Sim 60; Cov 40(Both); AA; bar,fly,foo  
      BBn     BBH           Sim 60; Cov 40(Both); NT; bar,fly,foo  
      CL      Closure       Sim 60; Cov 40(Both); AA               
      HT      BestHit       Sim 20; Cov 20; All; Description       
      OM      User Defined  orthoMCL.OM-40                         

   Sizes
      Prefix  =2   =3  4-5  6-10  11-15  16-20  21-25  >25  Total  #Seqs  
      BBa      0  155    0     0      0      0      0    0    155  65.8%  
      BBn      0  112    0     0      0      0      0    0    112  47.5%  
      CL      89  154    1     1      0      0      0    0    245  92.1%  
      HT      67  147    1     1      0      0      0    0    216  82.7%  
      OM      51  186    3     3      0      0      0    0    243  98.3%  

   Statistics
      Prefix  conLen  sdLen     Score1  SD    Score2  SD    
      BBa     525.69  49.69       0.47  0.07    0.82  0.12  
      BBn     498.04  31.27       0.48  0.07    0.86  0.11  
      CL      558.89  52.54       0.48  0.08    0.79  0.15  
      HT      600.58  72.62       0.47  0.10    0.79  0.16  
      OM      587.50  79.97       0.45  0.09    0.75  0.17  

PAIRS: 989
   Hits
      AA   Diff 847     Same 107      Similarity 72.8% (70.0%)  Coverage 81.7% (83.0%)
      NT   Diff 663     Same 4        Similarity 86.4% (87.0%)  Coverage 59.4% (63.7%)

   Aligned: 710   CDS: 995.7kb   5UTR: 69.6kb   3UTR: 106.5kb
      Codons         307.2k     Amino Acids                Nucleotides         
      Exact           58.1%     Exact            86.6%     CDS  Diff    24.6%  
      Synonymous      28.5%     Substitution >0   5.8%          Gaps     7.5%  
        Fourfold      14.7%     Substitution<=0   7.6%          SNPs    17.1%  
        Twofold       11.1%                                5UTR Diff    35.3%  
      Nonsynonymous   13.4%                                3UTR Diff    37.6%  

                     Pos1   Pos2   Pos3  Total                   GC  CpG-Nt  CpG-Cd  
      Transition     9.3%   5.0%  35.3%  49.7%       Both     38.1%    4.0%    2.2%  
      Transversion  11.9%   8.1%  30.3%  50.3%       Either   54.5%   11.3%    5.8%  
      ts/tv          0.78   0.62   1.16   0.99       Jaccard   0.70    0.35    0.38  

   KaKs method: YN    Pairs: 710
      Ka/Ks           Quartiles             Average            P-value       
      NA       19     Q1(Lower)   0.018     Ka       0.105     <1E-100  414  
      KaKs~1    0     Q2(Median)  0.040     Ks       2.667     <1E-10    96  
      KaKs<1  684     Q3(Upper)   0.109     P-value  0.038     <0.001    47  
      KaKs>1    7                                              Other    153  

SEQUENCES: 707
           Average  Lengths              %GC                     CpG O/E                
              5UTR      CDS   3UTR       5UTR    CDS   3UTR         5UTR    CDS   3UTR  
      bar    197.5   1560.2  255.0      40.7%  51.0%  39.2%        0.754  0.694  0.739  
      fly    145.2   1500.5  324.1      37.9%  46.6%  35.9%        0.747  0.695  0.657  
      foo    206.4   1497.0  366.4      40.8%  47.1%  37.4%        0.766  0.703  0.738  

   Counts  
                  C1       C2       C3  
      bar    812,745  665,939  853,758  
      fly    736,627  605,318  772,927  
      foo  1,009,851  706,578  537,403  

   Differential Expression (p-value < 0.001) 
           C1C2  C1C3  C2C3  
      bar     0    17    17  
      fly     0    16    14  
      foo     6    16    18  
----------------------------------------------------
PROCESSING:
AA: diamond --max-hsps 1 --masking 0 --sensitive --query-cover 25 --subject-cover 25
NT: blastn -evalue 1e-05 -max_hsps 1  -max_target_seqs 25
Score1: Sum-of-Pairs
Score2: Wentropy