| Label | Description | Compute
|
|---|
| Statistics
|
| Prefix | The cluster is referred to by this prefix in the various Filters
and Columns. | ---
|
| Method | The method used to compute the cluster. | See PROCESSING at end of Overview
|
| conLen | Average consensus length of the cluster. | Stats: Avg(col:conLen)
|
| sdLen | Average standard deviation of the sequence lengths (AA Len) in each
cluster. | Stats: Avg(col:sdLen)
|
| Score1 | Average of Score1.
See PROCESSING for the MSA score1 method. Default: Sum-of-pairs
| Stats: Avg(col:Score1)
|
| SD | Standard deviation of Score1
| Stats: StdDev(col:Score1)
|
| Score2 | Average of Score2.
See PROCESSING for the MSA score2 method. Default: Wentropy
| Stats: Avg(col:Score2)
|
| SD | Standard deviation of Score2
| Stats: StdDev(col:Score2)
|
| Sizes
|
| [Range]
| Range of cluster sizes per cluster set
| Calculate by sorting on the col:Count
|
| Label | Description | Compute
|
|---|
| Hits: (from hit file);
for the NT statistics, replace AA with NT.
|
| Diff
| The number of hits from different datasets.
| Filter: Hits: AA pairs;
Datasets: Different sets
|
| Same
| The number of hits from the same dataset.
| Filter: Hits: AA pairs;
Datasets: Same sets
|
| Similarity
| Average percent similarity.
| Filter: Hits: AA pairs; Stats: Avg(col:%AAsim)1
|
| Coverage
| Average percent coverage.
| Filter: Hits: AA pairs; Stats: (Avg(col:%AAcov1) + Avg(col:%AAcov2))/2)1
|
| Aligned:
Filter: Statistics: Has Stats (aligned using dynamic programming)
|
| CDS:
| Number of aligned CDS bases including gaps but not overhangs.
| Stats: Sum(col:Align)
|
| 5UTR:
| Number of aligned 5'UTR bases including gaps but not overhangs.
| View values; see2
|
| 3UTR:
| Number of aligned 3'UTR bases including gaps but not overhangs.
| View values; see2
|
| Codon column
|
| Codons
| Number of aligned codons excluding gaps.
| Stats: Sum(col:Calign)
|
| Exact
| Percent codons that are exactly the same.
| Stats: Avg(col:%Cexact)1
|
| Synonymous
| Percent codons that are synonymous (different codon, same amino acid).
| Stats: Avg(col:%Csyn)1
|
| Fourfold
| Percent codons that are fourfold (4d) (synonymous codons
where the ith position allows any of the 4 bases).
| Stats: Avg(col:%C4d)1
|
| Twofold
| Percent codons that are twofold (2d) (synonymous codons
where the ith position allows any of the 2 bases).
| Stats: Avg(col:%C2d)1
|
| Nonsynonymous
| Percent codons that are nonsynonynous (different amino acid).
| Stats: Avg(col:%nonSyn)1
|
| Amino acid column
|
| Exact
| Percent amino acid that are the same.
| Stats: Avg(col:%Aexact)1
|
| Substitution>0
| Percent amino acids that are substitutions with BLOSUM62>0.
| Stats: Avg(col:%Apos)1
|
| Substitution<=0
| Percent amino acids that are substitution with BLOSUM62<=0.
| Stats: Avg(col:%Aneg)1
|
| Nucleotides columns
|
| CDS Diff
| Percent CDS bases that are different, i.e. ((Gap+SNP)/Align)%.
| Stats: ((sum(col:gap) + sum(col:SNP)) / sum(col:align)) x 100.0
|
| Gaps
| Percent CDS bases that are Gaps, i.e. (Gaps/Align)%.
| Stats: (sum(col:gap) / sum(col:align)) x 100.0
|
| SNPs
| Percent CDS bases that are SNPs, i.e (SNP/Align)%.
| Stats: (sum(col:SNP) / sum(col:align)) x 100.0
|
| 5UTR Diff
| Percent 5'UTR bases that are different.
| Stats: Avg(col:%5diff)1
|
| 3UTR Diff
| Percent 3'UTR bases that are different.
| Stats: Avg(col:%3diff)1
|
| Columns: Pos1 Pos2 Pos3 Total
|
| Transition (ts)
| Percent SNPs that are transitions in each of the 3 codon positions.
| View values; see2
|
| Transversion (tv)
| Percent SNPs that are transversion in each of the 3 codon positions.
| View values; see2
|
| ts/tv
| The total number of transitions divided the total number of transversions
| View values; see2
|
Columns: GC CpG-Nt CpG-Cd
CpG-Nt (nucleotide) and CpG-Cd (codon, CpG does not cross codon boundaries).
|
| Both
| Percent CDS bases where both (union) sequences have a GC base.
Same for the CpG sites.
| View values; see2
|
| Either
| Percent CDS bases where either or both (intersection) sequences have a GC base.
Same for the CpG sites.
| View values; see2
|
| Jaccard
| The total number of 'both' divided by the total number of 'either'.
| View values; see2
|
| KaKs method:3
|
| KaKs
| It is rare for Ka/Ks to be exactly 1, so the following fudge factors are used:
| Rule | Fudge factor | Strength
| | KaKs>1 | >= 1.006 | positive (driving change)
| | KaKs=1 | >= 0.995 and < 1.006 | neutral
| | KaKs<1 | < 0.995 | purifying (against change)
|
| Set Pair Filters according to fudge factors on the left.
For NA, Filters: uncheck KaKs and check KaKs=NA
|
| Quartiles | Applies to the KaKs values. It uses the method of splitting the list in half;
Q1 is the median of the lower half and Q3 is the median of the upper half.
| Q2: Stats: Median(col:KaKs)
|
Average
| Ka | Nonsynonymous substitution rate. | Stats: Avg(col:Ka)
| | Ks | Synonymous substitution rate. | Stats: Avg(col:Ks)
| | P-value | KaKs p-value. | Stats: Avg(col:p-value)
| | P-value
| Counts of p-value in 4 ranges. | Sort on col:p-value. Round-off error occurs (see Display Decimal Help).
| |