Use NCBI reference sequence instead of pangolin

[EmilyHaag]

User suggestion from help email dated 7/21/23:

User suggests switching from pangolin reference data to NCBI sequence, as other resources use the NCBI sequence (BV-BRC, Covariant.org, Nextclade, and ViralZone).

"Between the pangolin and NCBI sequences, there are C8782T and T28144C. The former variant is silent, but the latter encodes ORF8:L84S, which means that the resources cited above and outbreak.info do not show the same data for ORF8 variants. Ultimately, outbreak.info cites ORF8:S84L for most variants, but other resources do not (except for some in ViralZone, which I took from outbreak.info without noticing the discrepancy; these will be corrected soon).
Would it be possible for you to swap the reference sequence so that all resources show the same variant positions for ORF8? This would eliminate the misleading ORF8:S84L shown in most of your variants and harmonize the data."

[emmahodcroft]

Thanks for creating the issue!