28e901dcf7f05026044feb8f4cc0fe9a267df7be
angie
  Sun Feb 4 09:21:18 2024 -0800
Mask the range 21610-21624 due to Ns/run-of-muts.  sars-cov-2-variants/lineage-proposals#1347

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 8fc850b..af269da 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -96,33 +96,33 @@
     # 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
-    sites: [ 21610,
-             21302, 21304, 21305, # https://github.com/sars-cov-2-variants/lineage-proposals/issues/1190
+    ranges: [ [ 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
+    sites: [ 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.