ea200cd254fbe9b6d231ee610ed51ed8c0eef899
angie
  Fri Jul 14 10:56:09 2023 -0700
Added comments about false mutations induced in XBD, XBP, XBR and XBS when placed in BA.5 and later in BA.2.75.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index f79de9b..502f7be 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -74,49 +74,59 @@
 
 BA.2.75:
     # Inherits BA.2 masking but has so many problems with false reversions I'm adding a ton here.
     representative: India/WB-INSACOG-1931503209307/2022
     reversions: [ # BA.2-level but not masked BA.2-wide to avoid messing up recombinants:
                   G670T, T2790C, T3037C, T4321C, G9424A, T9534C, T9866C, T10029C, T10198C,
                   G18163A, T19955C, G20055A, T21618C, G22200T, A22578G, T22674C, C22679T,
                   T22686C, G22688A, A22775G, T22813G, A22992G, A22995C, C23013A, G23055A,
                   T23063A, C23075T, G23403A, T23525C, G23599T, A23604C, T23948G, T24424A,
                   A24469T, T25000C, T26270C, G26577C, T27807C, T28271A, C29510A,
                   # BA.2.75-defining, very dropout-prone:
                   T4586C, G22001A, C22016T, A22033C, G22190A, C22577G, G26275A,
                   # BA.2.75-defining, bad but maybe not quite as bad:
                   T3796C, T3927C, T5183C, G12444A, A15451G, G22190A, A22331G, A22898G,
                   G22942T, C23013A ]
+    # False muts in re-placed (from BA.5) recombinants:
+    # XBD: A26275G
+    # XBP: G22331A, G22577C, G22898A, A26275G
+    # 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.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
+    # XBP: G12160A,
+    # XBR: G12160A
+    # XBS: G12160A
     reversions: [ G670T, T2790C, T3037C, A4184G, T4321C, G9424A, T9534C, T10198C, A12160G,
                   T15714C, T17410C, G18163A, T19955C, G20055A, T21618C, G22200T, A22578G,
                   T22674C, C22679T, T22686C, G22688A, A22775G, T22813G, G22882T, G22917T,
                   A22992G, A22995C, C23013A, G23018T, G23055A, T23063A, C23075T, G23403A,
                   T23525C, G23599T, A23604C, T25000C, A26529G, G26577C, A26709G, T27807C,
                   T27889C, T28271A, C29510A ]
 
 BQ.1:
     # Inherits from BA.5
     # Mask some suspicious run-of-nearby-site mutations that cause a mini-BQ.1 branch and
     # caused trouble when minimizing the tree for pango-designation v1.18.1 pangolin-data release.
     representative: England/PHEP-YYGYEQS/2022
     sites: [ 114, 117, 244, 256, 258, 261, 264 ]
 
 BQ.1.1: