##Supplemental Data 5: The interspecific DNA polymorphism across 12 Morus species cp genomes.

Input Data File: Z:\...\12_Morus_aligned.fas
 Number of sequences: 12    Number of sequences used: 12
 Selected region: 1-162710   Number of sites: 162710
 Total number of sites (excluding sites with gaps / missing data): 155976

 Number of polymorphic (segregating) sites, S: 2198
 Total number of mutations, Eta: 2241

 Number of Haplotypes, h: 12
 Haplotype (gene) diversity, Hd: 1.000
    Variance of Haplotype diversity: 0.00116
       Standard Deviation of Haplotype diversity: 0.034

 Nucleotide diversity, Pi: 0.00319
 Theta (per site) from Eta: 0.00476

 Theta (per site) from S, Theta-W: 0.00467
    Variance of theta (no recombination): 0.0000032
       Standard deviation of theta (no recombination): 0.00178
    Variance of theta (free recombination): 0.0000000
       Standard deviation of theta (free recombination): 0.00010

 Finite Sites Model 
    Theta (per site) from Pi: 0.00320
    Theta (per site) from S: 0.00471
    Theta (per site) from Eta: 0.00478

 Average number of nucleotide differences, k: 497.667
    Stochastic variance of k (no recombination), Vst(k): 43548.147
    Sampling variance of k (no recombination), Vs(k): 8903.805
       Total variance of k (no recombination), V(k): 52451.952
    Stochastic variance of k (free recombination), Vst(k): 165.889
    Sampling variance of k (free recombination), Vs(k): 30.162
       Total variance of k (free recombination), V(k): 196.051

 Theta (per sequence) from S, Theta-W: 727.844
    Variance of theta (no recombination): 77505.198
    Variance of theta (free recombination): 241.018

 Sliding Window Option
 Sites with alignment gaps were not counted in the window length (and slide)
   Window length: 500     Step size: 250






 Input Data File: Z:\...\12_Morus_aligned.fas
 Number of sequences: 12    Number of sequences used: 12
 Selected region: 1-162710   Number of sites: 162710
 Total number of sites (excluding sites with gaps / missing data): 155976

   Sites with alignment gaps or missing data: 6734
   Invariable (monomorphic) sites: 153778
   Variable (polymorphic) sites: 2198   (Total number of mutations: 2241)
      Singleton variable sites: 1579
      Parsimony informative sites: 619

      Singleton variable sites (two variants): 1554
      Parsimony informative sites (two variants): 602
      Singleton variable sites (three variants): 24
      Parsimony informative sites (three variants): 17
      Singleton variable sites (four variants): 1
      Parsimony informative sites (four variants): 0

 Protein Coding Region assignation:  No