Description of statistics on MLOGD results page:

1. non-reference name: Non-reference sequence name. Each table row lists statistics for a reference sequence versus non-reference sequence pairwise sequence comparison.
   
   
2. total # nt: Total number of non-reference sequence nucleotides that align with the reference sequence within the query nucleotide range. I.e. number of alignment columns which are not gapped, or ambiguous nt codes, in either the reference or non-reference sequence.
   
   
3. total # muts: Total number of point nucleotide differences between the non-reference sequence and the reference sequence, within the query nucleotide range.
   
   
4. divergence (muts / nt): Pairwise reference sequence to non-reference sequence divergence (mean number of point differences per nucleotide). (I.e. all nucleotide positions mutation fraction.) Equals column 3 / column 2.
   
   
5. # nt used: Number of nucleotides used to calculate the log likelihood scores. This will depend on the nucleotide range selected on the initial MLOGD server page, and will be reduced if any nucleotide positions are omitted due to gaps or ambiguous nt codes (in either reference or non-reference sequence), or stop to non-stop transitions (in either the null or alternate models).
   
   
6. MLOGD ln(LR) / nt: The sum of the null versus alternate model log likelihood ratios over the whole pairwise sequence comparison, divided by the number of nucleotides used.
   
   
7. frac null muts: Fraction of the aligned codons, within the null model CDSs, that are identical between the two sequences.
   
   
8. frac syn muts: Fraction of the aligned codons, within the null model CDSs, that are different between the two sequences but code for identical amino acids. (I.e. synonymous codon mutation fraction.)
   
   
9. frac nonsyn muts: Fraction of the aligned codons, within the null model CDSs, that are different between the two sequences and code for different amino acids. (I.e. nonsynonymous codon mutation fraction.)
   
   
10. frac N1 muts: Fraction of the 1st codon position nucleotides (e.g. the C in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 1st codon position mutation fraction.)
    
    
11. frac N2 muts: Fraction of the 2nd codon position nucleotides (e.g. the A in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 2nd codon position mutation fraction.)
    
    
12. frac N3 muts: Fraction of the 3rd codon position nucleotides (e.g. the G in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 3rd codon position mutation fraction.)
    
    

Notes:

• Columns 7 + 8 + 9 sum to one, unless the null model has no CDSs annotated, in which case all three values are zero.
• If the entire alignment is coding in the null model, then the average of columns 10, 11 and 12 is the pairwise sequence divergence, column 4. If the null model has no CDSs annotated then columns 10, 11 and 12 are zero.
• Multiplying column 6 by column 5 gives the log likelihood ratio for the whole pairwise sequence comparison. Positive values favour the alternate model, while negative values favour the null model.