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usher_masked_sites.yaml
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# Masking manually extracted from the UShER mask at:
# https://github.com/ucscGenomeBrowser/kent/blob/3ed65430d066888a23f7f97ebbc11eac3269586b/src/hg/utils/otto/sarscov2phylo/maskDelta.sh
# see also: https://github.com/yatisht/usher/issues/312#issue-1503004919
#
# Below specifies clades and what sites are masked in those clades. This information was manually
# extracted from the above script. We don't worry about the UTR masks as those don't include
# protein sequences for our amino-acid fitness level estimates.
mask_1:
clades:
# Delta
- 21A
- 21I
- 21J
sites:
- 22027
- 22028
- 22029
- 22030
- 22031
- 22032
- 22033
- 22034
- 28246
- 28247
- 28248
- 28249
- 28250
- 28251
- 28252
- 28253
- 28271
- 21846
- 21302
- 21304
- 21305
- 28254
- 28461
mask_2:
clades:
# Alpha
- 20I
# Beta
- 20H
# Gamma
- 20J
# BA.2
- 21L
- 22A
- 22B
- 22C
- 22D
- 22E
- 22F
sites:
- 11288
- 11289
- 11290
- 11291
- 11292
- 11293
- 11294
- 11295
- 11296
mask_3:
clades:
# BA.1
- 21K
sites:
- 11283
- 11284
- 11285
- 11286
- 11287
- 11288
- 11289
- 11290
- 11291
- 6513
- 6514
- 6515
- 21765
- 21766
- 21767
- 21768
- 21769
- 21770
- 21988
- 21989
- 21990
- 21991
- 21992
- 21993
- 21994
- 21995
- 22194
- 22195
- 22196
- 22197
- 22198
- 22199
- 22200
- 22201
- 22202
- 22203
- 22204
- 22205
- 22206
- 22207
- 22208
- 22209
- 22210
- 22211
- 22212
- 22213
- 22214
- 22215
- 22216
- 22217
- 28362
- 28363
- 28364
- 28365
- 28366
- 28367
- 28368
- 28369
- 28370
- 22813
- 22898
- 22882
- 23854
mask_4:
clades:
# BA.2
- 21L
- 22A
- 22B
- 22C
- 22D
- 22E
- 22F
sites:
- 197
- 198
- 199
- 200
- 201
- 203
- 204
- 206
- 207
- 214
- 216
- 217
- 218
- 219
- 221
- 222
- 223
- 224
- 225
- 228
- 230
- 231
- 232
- 233
- 239
- 241
- 242
- 243
- 245
- 246
- 29766
mask_5:
clades:
# BA.4
- 22A
# BA.5
- 22B
- 22E
sites:
- 21765
- 21766
- 21767
- 21768
- 21769
- 21770
mask_6:
clades:
# BA.2
- 21L
- 22A
- 22B
- 22C
- 22D
- 22E
- 22F
sites:
- 28877
- 28878
mask_7:
clades:
# BA.4
- 22A
sites:
- 686
- 687
- 688
- 689
- 690
- 691
- 692
- 693
- 694
mask_8:
clades:
# BA.2.75
- 22D
sites:
- 670
- 2790
- 3037
- 4321
- 9424
- 9534
- 9866
- 10029
- 10198
- 18163
- 19955
- 20055
- 21618
- 22200
- 22578
- 22674
- 22679
- 22686
- 22688
- 22775
- 22813
- 22992
- 22995
- 23013
- 23055
- 23063
- 23075
- 23403
- 23525
- 23599
- 23604
- 23948
- 24424
- 24469
- 25000
- 26270
- 26577
- 27807
- 28271
- 29510
- 4586
- 22001
- 22016
- 22033
- 22190
- 22577
- 26275
- 3796
- 3927
- 5183
- 12444
- 15451
- 22190
- 22331
- 22898
- 22942
- 23013
mask_9:
clades:
# BA.5
- 22B
- 22E
sites:
- 670
- 2790
- 3037
- 4184
- 4321
- 9424
- 9534
- 10198
- 12160
- 15714
- 17410
- 18163
- 19955
- 20055
- 21618
- 22200
- 22578
- 22674
- 22679
- 22686
- 22688
- 22775
- 22813
- 22882
- 22917
- 22992
- 22995
- 23013
- 23018
- 23055
- 23063
- 23075
- 23403
- 23525
- 23599
- 23604
- 25000
- 26529
- 26577
- 26709
- 27807
- 27889
- 28271
- 29510