La Braña 2 and modern European variation

This is a reanalysis of the La Braña's but this time separately. The La Braña 2 matched the 1000 genome reference panel with 56k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 56k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 26k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 21k SNP's.

The heatmap, tree structure and PCA plot below shows somewhat different result than for the La Braña 1 as La Braña 2 appears to have a position that cluster around with the Scandinavian-Saamis (individuals with both Scandinavian and Saami background).

This means that the original analysis of the composite La Braña need to be adjusted after the findings here. La Braña 2 appears most similar to individuals of mixed Scandinavian and Saami ancestry..

CC Euro unlinked 21k

 CC Euro unlinked 21k detailed 

 CC Euro unlinked 21k D1-D2

  CC Euro unlinked 21k D1-D3

EDIT: 20/9-13

Download BRA2 individual results