snp_candidates.html:
Contains a list of putative SNPs. All SNPs are supported by at least
two ESTs and present in more than 2 % of the ESTs covering that
particular position of a cluster. Multiple SNPs might be present at a
given position, see eg. Ss1.1-Utr1-UTR010049E05.5
around position 1080. Here two distinct variations are present
('C-------C----C----------' and 'C-----------'). This means that the
variations are linked. That is, two distinct possible variations are
found in the data, one ('C-----------') has a C instead of a T, but is
otherwise identical to the consensus, the other contains C's at
positions 1, 9, and 14 instead of the relevant consensus bases. This
also show that every EST that has the C substitutions at position 1 and
9, also has the substitution at position 14.
If a 12-mer word has more than 4 bases where it's different from
the consensus, all 12 bases are reported. An example of this is Ss1.1-rova027_e10.5
(around position 300, SNP '-----A----------------TGCAGGAAAACCAA'),
where a phylogenetic variant has an 'A' substitution (at postion 306),
but further along larger variations. Looking at the EST-sequences you can
see that this is due to both base substitutions and indels, therefore
setting this variant apart from a classic SNP.