c1d527b5f7544b6a5a3fc0bf49938ae61955a1a8
angie
  Tue Mar 5 11:00:42 2024 -0800
More masked sites in BA.2.86 from inspection of tree in taxonium, and JN.1 from github issue.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index c31b082..c13e0a9 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -96,39 +96,53 @@
     # XBS: A22190G, G22331A, G22577C, G22898A, A26275G
 
 BN.1.2.3:
     # Inherits from BA.2.75
     representative: England/QEUH-326228D4/2022
     sites: [ 337 # https://github.com/cov-lineages/pango-designation/issues/2016#issuecomment-1626159006
            ]
 
 BA.2.86:
     # Inherits from BA.2
     # @Over-There-Is requested 21610 - very messy indeed.
     # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606#issuecomment-1801095482
     # @aviczhl2 pointed out some recurring reversions:
     # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1072
     representative: OY747147.1
-    ranges: [ [ 21765, 21770 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606
+    ranges: [ [ 21294, 21296 ],  # run of muts, makes a mini-JN.1
+              [ 21539, 21542 ],  # run of muts, France/...-HCL, makes a mini-JN.1
+              [ 21765, 21770 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606
               [ 21610, 21624 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1347
               [ 21625, 21631 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1380
               [ 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 ]
+    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
+            ]
 
 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