Summary of errors in Nextclade

[AnonymousUserUse]

Hi @corneliusroemer just to highlight something went wrong with the last nextclade updates:

BL.1.3 : it is defined by S:F490L and it is around 27 sequences but the nextclade BL.1.3 query on covspectrum finds 48 sequences and just a tiny bit with S:F490L
Nextclade for BL.1.3:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=BL.1.3
Real BL.1.3:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3ABA.2.75*+%26+S%3A346T+%26+S%3A574v+%26+S%3A490L

BN.3: it is defined by S:N450D and it is around 24 sequences but the nextclade BN.3 query on covspectrum finds 43 sequences and just a tiny bit with S:N450D
Nextclade for BN.3:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=BN.3
Real BN.3 (with S:N450D):
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AN450D&nextcladePangoLineage=BN.3&

BA.4.6.2: it is defined by S:V445A and it is around 75 sequences but the nextclade BA.4.6.2 query on covspectrum finds 146 sequences and just a tiny bit with S:V445A
Nextclade for BA.4.6.2:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=BA.4.6.2
Real BA.4.6.2 (with S:V445A):
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AV445A&nextcladePangoLineage=BA.4.6.2&

BQ.1.18: it is defined by S:Y144- and it is around 1194 sequences but the nextclade BQ.1.18 query on covspectrum finds 1795 sequences and just a tiny bit with S:Y144-
Nextclade for BQ.1.18:
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nextcladePangoLineage=BQ.1.18&
Real BQ.1.18 (with S:Y144-):
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?aaMutations=S%3A144-&nextcladePangoLineage=BQ.1.18&

BQ.1.28: it is defined by ins22303TCAAGATGGATG, C25096T and it is around 317 sequences but the nextclade BQ.1.28 query on covspectrum finds 3839 sequences and just a tiny bit with C25096T
Nextclade for BQ.1.28:
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nextcladePangoLineage=BQ.1.28&
Real BQ.1.28 (with C25096T):
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=C25096T&nextcladePangoLineage=BQ.1.28*&

[AnonymousUserUse]

@corneliusroemer
I have checked the Nextclade staging tree (https://nextstrain.org/staging/nextclade/sars-cov-2/21L) and noticed that the branch leading to BL.1.3, BN.3, BA.4.6.2, and BQ.1.18 has more than 2 mutations (not including 2 mutations, i.e. at least 3 mutations), so that only a part of mutations leading to the lineage have to be fulfilled to assign as that lineage. So it is probably the same problem as in #966.
Could this problem be fixed (eventually in mid-term), e.g. by defining certain mutations that have to fulfilled for the assignment of a certain lineage?