28c91a2f0848971d9f707c0a034c48f57757a4b5
angie
  Tue Dec 2 15:32:59 2025 -0800
Use new exclusions keyword to prevent real G23599T reversion from being masked under XFJ.3.1.
Change has been in place since Oct 29, just committing it now.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 9e243948459..25c285d0d5c 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -121,30 +121,35 @@
               [ 22194, 22196 ] ] # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1380
     sites: [ 58, 59,   # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089
              13427,    # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1313
              21302, 21304, 21305, # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1190
            ]
     reversions: [ T21711C, C22032T, A22033C, G22034A, A22770G, A23012G, G26610A,
                   # Added 2024-03-01 because they're causing reversion branches with >= 100 samples.
                   # Unfortunately 6183 and 9142 will be incorrect in XDD, XDR, XDS.
                   T2790C, T4321C, G6183A, T9142C, C13339T, A22353C, G22556A, C22577G, T22674C,
                   T22686C, G22688A, T22813G, C22895G, A22896T, A22898G, T22916C, G22917T, A22942T,
                   A23005T, C23075T, G23599T, G23604C, T24378C, T26858C,
                   # Added 2024-04-15 by request from Cornelius Roemer, doesn't affect currently
                   # designated recombinants fortunately:
                   T21941G,
                 ]
+    exclusions:
+      # Cornelius requested exclusion of XFJ.3.1, some of whose descendants have a real G23599T reversion.
+      # https://github.com/cov-lineages/pango-designation/commit/02d2cb6aa1155e4d0473fcb1ff345f472725be27
+      - site: 23599
+        representative: England/CLIMB-CM7YJM45/2025
 
 JN.1:
     # Inherits from BA.2.86
     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