39232e1eb0b5b78c0e3f6ea360a5f70195f70840
angie
  Thu Jun 6 10:53:05 2024 -0700
BA.2.86 representative has a name now.  I removed 21627 (S:22) from BA.2.86's masking at @FedeGueli's request (sequences with mutation there were removed and added back).

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 654206d..f325dbd 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -95,36 +95,38 @@
     # XBR: A22190G, G22331A, G22577C, G22898A, A26275G
     # 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
+    representative: Denmark/DCGC-661170/2023
     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
+              [ 21625, 21626 ],  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1380
+                                 # 21627 taken back out 2024-05-26 by email request from FedeGueli
+              [ 21628, 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,
                   # 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,
                 ]