29784b8ab0b8c9ae4f639d4411320ca0bbb3238b
angie
  Wed Aug 14 13:07:57 2024 -0700
Added a couple JN.1 GBW artifact sites reported by @FedeGueli.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index f325dbd..7022b12 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -125,30 +125,32 @@
                   # 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,
                 ]
 
 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
     reversions: [ T17334G        # Reversion of JN.1.11.1 mutation, email from FedeGueli
                 ]
 
 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: