Simple question: for determining the mutations in full genome measles sequences, which strain is used as the reference (root)? As far as I can tell so far it is one that is subtype A, but I’d like to know the precise accession number, so that I can do some analysis of my own.
Hi @roberthohan
That’s NC_001498.1 currently
For the 2 Nextstrain builds this is:
- complete genome: /phylogenetic/defaults/measles_reference.gb
- 450bp region (1233…1682) of the N gene: /phylogenetic/defaults/measles_reference_N450.gb
(see description and the rest of this GitHub repo for details)
For Nextclade dataset it’s the second one, in fasta format: /phylogenetic/defaults/measles_reference_N450.fasta. The resulting dataset is in github.com/nextstrain/nextclade_data/data/nextstrain/measles
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