error in spike sequence for HK.3.1

[jbloom]

@corneliusroemer, I think you have some sort of error in the spike mutations listed for HK.3.1 in the JSON file. The mutations listed in the JSON are as follows, and include no spike mutations after site 142. I think there should be spike mutations after site 142.

  "aaSubstitutions": [
   "E:T9I",
   "E:T11A",
   "M:Q19E",
   "M:A63T",
   "N:P13L",
   "N:R203K",
   "N:G204R",
   "N:S413R",
   "ORF1a:K47R",
   "ORF1a:S135R",
   "ORF1a:A690V",
   "ORF1a:T842I",
   "ORF1a:G1307S",
   "ORF1a:G1819S",
   "ORF1a:L3027F",
   "ORF1a:T3090I",
   "ORF1a:A3143V",
   "ORF1a:L3201F",
   "ORF1a:T3255I",
   "ORF1a:P3395H",
   "ORF1a:T4175I",
   "ORF1b:D54N",
   "ORF1b:P314L",
   "ORF1b:G662S",
   "ORF1b:S959P",
   "ORF1b:R1315C",
   "ORF1b:I1566V",
   "ORF1b:T2163I",
   "ORF3a:T223I",
   "ORF6:D61L",
   "ORF8:G8*",
   "ORF9b:I5T",
   "ORF9b:P10S",
   "S:T19I",
   "S:A27S",
   "S:Q52H",
   "S:V83A",
   "S:G142D"
  ],

[corneliusroemer]

Thanks, yes I saw there's a frame shift that the automatic consensus algorithm doesn't clean up, will fix through overwrite.

…

On Sun, Sep 10, 2023, 19:22 Jesse Bloom ***@***.***> wrote: @corneliusroemer <https://github.com/corneliusroemer>, I think you have some sort of error in the spike mutations listed for HK.3.1 in the JSON file <https://github.com/corneliusroemer/pango-sequences/blob/main/data/pango-consensus-sequences_summary.json>. The mutations listed in the JSON are as follows, and include no spike mutations after site 142: "aaSubstitutions": [ "E:T9I", "E:T11A", "M:Q19E", "M:A63T", "N:P13L", "N:R203K", "N:G204R", "N:S413R", "ORF1a:K47R", "ORF1a:S135R", "ORF1a:A690V", "ORF1a:T842I", "ORF1a:G1307S", "ORF1a:G1819S", "ORF1a:L3027F", "ORF1a:T3090I", "ORF1a:A3143V", "ORF1a:L3201F", "ORF1a:T3255I", "ORF1a:P3395H", "ORF1a:T4175I", "ORF1b:D54N", "ORF1b:P314L", "ORF1b:G662S", "ORF1b:S959P", "ORF1b:R1315C", "ORF1b:I1566V", "ORF1b:T2163I", "ORF3a:T223I", "ORF6:D61L", "ORF8:G8*", "ORF9b:I5T", "ORF9b:P10S", "S:T19I", "S:A27S", "S:Q52H", "S:V83A", "S:G142D" ], — Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF77AQICXARXJ2Q2JEDPKX3XZXZN3ANCNFSM6AAAAAA4SJYJNA> . You are receiving this because you were mentioned.Message ID: ***@***.***>