c1f41351d9731fd77bc1fcdbcd2f41a91ede93a0
angie
  Sun Jul 23 15:11:31 2023 -0700
Mask noisy sites 21994, 21995, 21998 in XBB (starting 2023-07-21 build).  Pick a new representative for XBB.1.5 since order of mutations was switched (now T17124C > T23018C).

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index 502f7be..f5135f4 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -126,39 +126,43 @@
     # 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:
     # Inherits from BQ.1
     representative: England/DHSC-CYF1KSU/2022
     reversions: [ C22893A, A22942T ]
 
 XBB:
     # Inherits from BA.2
     # Lots of false reversions; I would also mask G405A except that would be wrong for XBN.
     representative: BGD/icddrb_TND_06_1053/2022
+    # Homopolymer run 21999-22005 causes big trouble for Ion Torrent & nanopore, leading to false
+    # substitutions in 21994, 21995 and 21998 as discussed in pango-designation issues 1882, 1503,
+    # 1999, 1918.  21998 in particular crops up a lot, all over XBB, interfering with many sublins.
+    sites: [ 21994, 21995, 21998 ]
     reversions: [ T2790C, T3037C, A4184G, T4321C, T9344C, G9424A, T10198C, C17859T, G19326A,
                   T21618C, C21810T, A22000C, G22109C, C22577G, A22578G, C22599G, A22664C, C22679T,
                   T22686C, G22688A, T22813G, C22895G, C22896T, A22898G, G22942T, A22992G, A22995C,
                   C23013A, C23019T, C23031T, T24424A, A24469T, T25000C, T26060C, G26577C, A26709G,
                   T26858C, T27807C ]
 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-326C0A5A/2023
+    representative: England/BRBR-32671539/2023
     reversions: [ T27915G ]
 
 XBC:
     # Inherits nothing!  Should find out its deletions.
     # 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
     reversions: [ G5584A, T13019C, T22329C, T25000C, C27718T, T28271A ]