366028b554770e59a35f881811dd006c047ce9c6
angie
  Thu Dec 4 15:32:59 2025 -0800
Added RE.1.1 reversions and site requested by @ryhisner

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 25c285d0d5c..5737b7d37ce 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -153,30 +153,37 @@
 KP.1:
     # Inherits from JN.1
     representative: England/CLIMB-CM7YEN1U/2024
     reversions: [ T17334G        # Reversion of JN.1.11.1 mutation, email from FedeGueli
                 ]
 
 KP.3.1.1:
     # Inherits from JN.1
     representative: England/CLIMB-CM7YJCHG/2024
     reversions: [ C22926T,  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1914
                   C22928T,  # ''
                   # Others I noticed while looking at the above:
                   G7842A, T23948G, C3565T, T17334G, G19722A, G23055A, T28271A, T23063A, G22910A
                 ]
 
+RE.1.1:
+    # No inheritance -- BA.3.2 descendant with lots of dropout in Australia/WA sequences
+    # https://github.com/sars-cov-2-variants/lineage-proposals/issues/3093#issuecomment-3508425340
+    representative: Australia/WA17392/2025
+    reversions: [ A336G, C13375T, C22629A, T28996A ]
+    sites: [ 28254 ]
+
 BA.4:
     # BA.4 is placed on the BA.2 branch so it inherits all the BA.2 sites.
     representative: SouthAfrica/NICD-N41664/2022
     ranges: [ [ 686, 694 ], [ 21765, 21770 ] ]
 
 BA.5:
     # BA.5 is placed on the BA.2 branch so it inherits all the BA.2 sites.
     representative: England/PHEP-YYFJPAM/2022
     ranges: [ [ 21765, 21770 ] ]
     # Some of these should be reverted in recombinants, but we're pretty much past the point of
     # simultaneous Delta/Omicron and the noise from false reversions is so intolerable that we'll
     # just have to watch out for missing reversions when working with recombinants.
     # False muts in recombinants that were later re-placed in BA.2.75:
     # XBD: G12160A, T22917G, T23018G
     # XBP: G12160A,