Overview
Concordance analysis allows us to group strains that are genetically almost identical into an isotype. The following table summarizes the number of isotypes from previous and current releases, and the number of strains that belong to those isotypes.
| Isotypes | Strains | Strains with WGS data | Strains with RAD-seq data | |
|---|---|---|---|---|
| Previous Release | 550 | 1523 | 1383 | 140 |
| Current Release | 61 | 234 | 234 | -2* |
| Total | 611 | 1755 | 1617 | 138 |
*Two strains (JU262 and JU263) were sequenced in this set, previously only sequenced with RAD-seq
Concordance score distribution and cutoff
We examined the pairwise concordance scores of all strains. Concordance values for every pair of strains were calculated as the number of shared variant sites divided by the total number of variants called for each pair. If the concordance score was more than 0.9997, the strain pair is grouped into the same isotype.
Search for concordance for strain pairs
Strain comparisons are listed in the table below. Only concordance scores > 0.999 are shown.
- ECA2649 had high concordance to two distinct isotype groups. However, upon investigating the relationships to each group, we chose to manually place ECA2649 with isotype ECA2551, not ECA2672.
- Keep previous isotypes JU2600 and JU1793 separate
Changes from previous release
- JU262 and JU263 have now been whole-genome sequenced (previously RAD-sequenced), and thus their release dates have updated to 20231213