JG.3+Orf1b:A2268S+S:T51I(59 seqs, 9 countries)

[xz-keg]

JG.3+G20269T(Orf1b:A2268S),C21714T(S:T51I)

GISAID query: G20269T,C21714T,C23673T No. of seqs: 31(Denmark 2 UK 2 Finland 2 France 10 Italy 8 Spain 5 Switzerland 1) 30 from this query, EPI_ISL_18411927 shares mutations while having S:51 missing coverage. (now 3)

First: EPI_ISL_18468089, Spain, 2023-9-21 Latest: EPI_ISL_18540045, Denmark, 2023-11-13

usher

Usher put this in two branches because EPI_ISL_18411927 has S:51 missing coverage while sharing mutations with one branch , causing the tree to split. The correct order shall be S:T51I at first and then separate into two branches.

[AngieHinrichs]

It is not only EPI_ISL_18411927, there are actually 3 sequences from Italy in the 2023-11-26 tree that have G20269T and C3535T but not (apparently) C21714T. Here is a view where samples are colored by allele at 21724 (green = T, orange = C):

When you say "EPI_ISL_18411927 has S:51 masked", do you mean it has an N at 21724 instead of C or T? That is different from masking -- it means that the genome sequencing was missing information or had inconsistent data at that position.

I see that all three of EPI_ISL_18411927, EPI_ISL_18542033, and EPI_ISL_18542042 have N at 21714. So I will try a prune/re-opt/re-place.

[xz-keg]

It is not only EPI_ISL_18411927, there are actually 3 sequences from Italy in the 2023-11-26 tree that have G20269T and C3535T but not (apparently) C21714T. Here is a view where samples are colored by allele at 21724 (green = T, orange = C): When you say "EPI_ISL_18411927 has S:51 masked", do you mean it has an N at 21724 instead of C or T? That is different from masking -- it means that the genome sequencing was missing information or had inconsistent data at that position.

I see that all three of EPI_ISL_18411927, EPI_ISL_18542033, and EPI_ISL_18542042 have N at 21714. So I will try a prune/re-opt/re-place.

Thanks.

Yeah, to be accurate, shall use the term "missing coverage".

[xz-keg]

41, USA

[xz-keg]

47, Germany

[FedeGueli]

Lets see how much it takes to arrive at 100

[FedeGueli]

slow closing it down