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@NkRMnZr isnt this one of the lineages you dropped tracking due to suspicious sartefact/misplacement?
Yes, there's flip-flop so it is not tracked by sars-cov-2-variants/lineage-proposals#537 anymore. Since C27059T is also related to another FLip lineage XBB.1.5.70, I had a thought it was involved in some kind of recombinant event, perhaps that's the reason why C27059T and other flip-flops are so persistent in UShER tree.
This is also related to a part of Branch 5 of sars-cov-2-variants/lineage-proposals#787 as you mentioned, I haven't added -C27059T to that query, cause the Russian seqs with or without C27059T looks to be the same FLippeR lineage (can't confirm, either). C27059T designation complitated things a bit, before the UShER tree finally resolved.
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Good spot with the branch that should be in HK.30 -- I missed that tonight but will try to fix it soon.
@FedeGueli Actually it is kind of stubborn and does not want to move because it's on a branch with hundreds of sequences that has C27507T first (though not >1000 sequences like the HK.30 branch). I don't think there's enough information to distinguish between an independent occurrence of C27507T vs T26609C vs recombination - ? I think I could force it to move by temporarily pruning hundreds of sequences with C27507T, but I usually don't make such big cuts unless I'm more sure. Another possibility would be to add a label HK.30_27507T on your branch. Or we could just leave it as a mystery. 🙂 What would you prefer?
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Good spot with the branch that should be in HK.30 -- I missed that tonight but will try to fix it soon.
@FedeGueli Actually it is kind of stubborn and does not want to move because it's on a branch with hundreds of sequences that has C27507T first (though not >1000 sequences like the HK.30 branch). I don't think there's enough information to distinguish between an independent occurrence of C27507T vs T26609C vs recombination - ? I think I could force it to move by temporarily pruning hundreds of sequences with C27507T, but I usually don't make such big cuts unless I'm more sure. Another possibility would be to add a label HK.30_27507T on your branch. Or we could just leave it as a mystery. 🙂 What would you prefer?
I think adding a label will be wonderful! Thank you very much Angie as always!
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@NkRMnZr isnt this one of the lineages you dropped tracking due to suspicious sartefact/misplacement?
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solved via @aviczhl2 sars-cov-2-variants/lineage-proposals#861
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Yes, there's flip-flop so it is not tracked by sars-cov-2-variants/lineage-proposals#537 anymore. Since
C27059Tis also related to another FLip lineageXBB.1.5.70, I had a thought it was involved in some kind of recombinant event, perhaps that's the reason whyC27059Tand other flip-flops are so persistent in UShER tree.This is also related to a part of Branch 5 of sars-cov-2-variants/lineage-proposals#787 as you mentioned, I haven't added
-C27059Tto that query, cause the Russian seqs with or withoutC27059Tlooks to be the same FLippeR lineage (can't confirm, either).C27059Tdesignation complitated things a bit, before the UShER tree finally resolved.6e3305fThere was a problem hiding this comment.
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THX!
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@NkRMnZr and @aviczhl2 cc @AngieHinrichs
I met back this 27507 thing and i had a bit more time to look at it: A27507C is defining of XBB.1.9.2 and it mutated in just 300 sequences of XBB.1.9.2 to T these encompass both formerly HK.32.1 and the EG.5.1+T26609C+ S:T478R that should be HK.30 but is misplaced to EG.5.1.1 branch with the former HK.32.1 :
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_a8b0_f6a560.json?c=gt-nuc_27507&gmax=28507&gmin=26507&label=id:node_3418986
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Good spot with the branch that should be in HK.30 -- I missed that tonight but will try to fix it soon.
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@FedeGueli Actually it is kind of stubborn and does not want to move because it's on a branch with hundreds of sequences that has C27507T first (though not >1000 sequences like the HK.30 branch). I don't think there's enough information to distinguish between an independent occurrence of C27507T vs T26609C vs recombination - ? I think I could force it to move by temporarily pruning hundreds of sequences with C27507T, but I usually don't make such big cuts unless I'm more sure. Another possibility would be to add a label HK.30_27507T on your branch. Or we could just leave it as a mystery. 🙂 What would you prefer?
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