Need to update mutation lists for several other lineages

[ArtPoon]

• [ ] BA.5.2.1
• [ ] BA.5.2
• [ ] BF.7
• [ ] BA.5.1
• [ ] BQ.1 ( expand BQ.1.1 ?)
• [ ] BA.4.6
• [ ] BF.10
• [ ] BF.11
• [ ] XBB (we can't call recombinants easily)

[ArtPoon]

maybe we should just start running Freya instead of having to chase sub-lineages all the time

[ArtPoon]

@Abayomi-Olabode @GopiGugan - I've written an R script (unique-mutations.R) that will process the JSON file generated by our Untitled project to:

1. determine the frequencies of mutations in genomes that belong to some focus lineage X
2. generate a barplot of frequencies for those mutations in all other (non-focal) lineages

Example for BA.5.2.1:

[ArtPoon]

I'll copy my current JSON file to /data/wastewater so you don't have to generate it yourself (but you just have to run Untitled retrieve.py to do so)

[ArtPoon]

Note the above plot is displaying the mean mutation frequencies, averaged across other lineages. If there is a handful of lineages that are fixed for the same mutation, it may still be shown as a low frequency.

[ArtPoon]

This might be more useful:

max.freq <- apply(others, 2, function(x) row.names(others)[which.max(x)])

[Abayomi-Olabode]

Thanks