8206caf3deee5603597c6fdbcae1320afc37281a
angie
  Sat Dec 23 18:25:37 2023 -0800
Additional sites/ranges for BA.2.86 and XBC.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 1a51e1c..8fc850b 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -96,31 +96,34 @@
     # 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
-    sites: [ 21610 ]
+    ranges: [ [ 21765, 21770 ] ]  # https://github.com/sars-cov-2-variants/lineage-proposals/issues/606
+    sites: [ 21610,
+             21302, 21304, 21305, # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1190
+           ]
     reversions: [ T21711C, C22032T, A22033C, G22034A, A23012G, G26610A ]
 
 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:
@@ -166,28 +169,30 @@
 XBB.1:
     # Inherits from XBB
     # Here I'm going a bit past the technical start of XBB.1, to include G27915T to be more sure
     # that it's XBB.1 before we mask out the defining mutation of XBB.1
     representative: England/LSPA-32578111/2022
     reversions: [ T22317G ]
 
 XBB.1.5:
     # Inherits from XBB.1
     # Don't believe reversions on 27915 once we're as far as XBB.1.*
     representative: England/BRBR-32671539/2022
     reversions: [ T27915G ]
 
 XBC:
     # Inherits nothing!  Should find out its deletions.
+    # Deletion 22289-22294 pointed out in #2405.
     # Cornelius Roemer requested to mask several reversions in
     # https://github.com/cov-lineages/pango-designation/issues/1100#issuecomment-1426502678
     representative: Philippines/PH-VUI-142736/2022
+    ranges: [ [ 22289, 22294 ] ]
     reversions: [ G5584A, T13019C, T22329C, T25000C, C27718T, T28271A ]
 
 XCK:
     # Inherits from XBB.1.5
     # @FedeGueli pointed out that the usher tree had a very flaky 29729. TL;DR mafft is counfounding
     # two nearby deletions, a new 29726 and the old 29734-29759, and making a false subst by getting
     # the deletion boundaries wrong.  Mask 29729 here.
     representative: USA/TX-CDC-QDX84451512/2023
     representativeBacktrack: 2
     sites: [ 29729 ]