5ae4d83b976b96f74cc3e1846e525601b6473cb3
angie
  Fri Mar 15 13:43:16 2024 -0700
Expand masked range for JN.1 after more discussion in cov-lineages/pango-designation#2510

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index c13e0a9..116f1a6 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -117,31 +117,31 @@
     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,
                 ]
 
 JN.1:
     # Inherits from BA.2.86
     representative: Denmark/DCGC-661561/2023
-    ranges: [ [ 23009, 23011 ],  # https://github.com/cov-lineages/pango-designation/issues/2510
+    ranges: [ [ 23008, 23011 ],  # https://github.com/cov-lineages/pango-designation/issues/2510
             ]
 
 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: