5793028c4b37b6cb8300580e70d7b078abc516b2
angie
  Wed Oct 4 17:46:58 2023 -0700
Mask deletion 21991-21993 in XBB.

diff --git src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
index cf04d29..0e3e5d7 100644
--- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
+++ src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
@@ -129,31 +129,34 @@
     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 ]
+    # Also, XBB.1.9, XBB.1.16 and XBB.2.3 sequences all seem to have del21991-21993 though very few
+    # XBB.1.5 polytomy sequences seem to have it.  Mask anyway, causing trouble.
+    ranges: [ [ 21991, 21995 ] ]
+    sites: [ 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.*