9804a48d4ee019ce876c5eb2f98239830a2ef766
angie
  Tue Sep 10 14:03:32 2024 -0700
Mask artifactual reversions in KP.3.1.1.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 7022b12..1096625 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -136,30 +136,39 @@
     representative: Denmark/DCGC-661561/2023
     ranges: [ [ 23008, 23011 ],  # https://github.com/cov-lineages/pango-designation/issues/2510
             ]
     sites: [ 1871,          # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1466
              1368,          # GBW artifact, email from FedeGueli
              6569,          # ''
              17562,         # very homoplasic (or systematic error?) in JN.1, email from FedeGueli
            ]
 
 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
+                ]
+
 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,