I have been comparing designated lineages for sequences in lineages.csv with those sequences' assigned lineages from the UCSC UShER tree, and while they mostly agree, I have found several lineages for which many of their designated sequences are placed on a child lineage branch in the UShER tree. For example, 44 out of 422 designated sequences for XBB.1.9 are placed on the XBB.1.9.4 branch in the UShER tree. The most extreme example is BQ.1.3, for which 1109 out of 1215 designated sequences are placed on the BQ.1.3.2 branch.
@corneliusroemer How would you like to proceed with these? Should I go ahead and update designations in lineages.csv based on UShER tree placements, or do you have more stringent filtering methods that you would rather apply to lists of suggested updates?
Here is a summary of lineages with a significant (>= ~10%, except for the last 3) proportion of designated sequences that now belong to child lineages:
I have been comparing designated lineages for sequences in lineages.csv with those sequences' assigned lineages from the UCSC UShER tree, and while they mostly agree, I have found several lineages for which many of their designated sequences are placed on a child lineage branch in the UShER tree. For example, 44 out of 422 designated sequences for XBB.1.9 are placed on the XBB.1.9.4 branch in the UShER tree. The most extreme example is BQ.1.3, for which 1109 out of 1215 designated sequences are placed on the BQ.1.3.2 branch.
@corneliusroemer How would you like to proceed with these? Should I go ahead and update designations in lineages.csv based on UShER tree placements, or do you have more stringent filtering methods that you would rather apply to lists of suggested updates?
Here is a summary of lineages with a significant (>= ~10%, except for the last 3) proportion of designated sequences that now belong to child lineages: