/
exclude.txt
200 lines (179 loc) · 4.29 KB
/
exclude.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
# Duplicate of Guangdong/20SF012/2020 / EPI_ISL_403932
HKU-SZ-002a_2020
# Duplicates of USA/WA1/2020
USA/WA1-F6/2020
USA/WA1-A12/2020
# Duplicates of Wuhan/IVDC-HB-envF13/2020
Wuhan/IVDC-HB-envF13-20/2020
Wuhan/IVDC-HB-envF13-21/2020
# Duplicates of Italy/INMI1-cs/2020
Italy/INMI1/2020
Italy/INMI1-isl/2020
# Duplicates of France/IDF0372/2020, France/IDF0515/2020 and France/IDF0386-islP1/2020
France/IDF0372-isl/2020
France/IDF0515-isl/2020
France/IDF0386-islP3/2020
# Appears to be a duplicate of France/IDF0515/2020 47F taken 3 days later on Feb 2
France/IDF0571/2020
# Presumed early submission of the now-included Shenzhen/HKU-SZ-005/2020. Formerly a lack of precise date lead to an incorrect time placement (end of Jan)
HKU-SZ-005b_2020
# Unknown precise date (2020-01-XX). Travel history shows Hubei, so may be good to rerun and see how this fits.
SouthKorea/SNU01/2020
# Doesn't have the enough divergence relative to supposed sampling date
Hefei/2/2020
# Seems divergent - sample date 8 Jan, but 6 muts from root.
Jingzhou/HBCDC-HB-01/2020
# Far to divergent- 30 mutations
Wuhan/HBCDC-HB-04/2019
# Missing mutations
Netherlands/Oisterwijk_1364072/2020
Netherlands/Utrecht_1364066/2020
# Confusing phylogeography
Netherlands/Rotterdam_1363790/2020
Netherlands/NoordBrabant_5/2020
# Missing precise date
Netherlands/NoordBrabant_34/2020
# These have more tip-specific divergence than expected
Beijing/IVDC-BJ-005/2020
China/WF0023/2020
Henan/IVDC-HeN-002/2020
Guangdong/GDSZ202013-P0014/2020
Shanghai/IVDC-SH-001/2020
Shenzhen/SZTH-001/2020
Shenzhen/SZTH-004/2020
Wuhan/IPBCAMS-WH-05/2020
Wuhan/IVDC-HB-envF54/2020
Wuhan/WH02/2019
Guangzhou/GZMU0016/2020
Guangzhou/GZMU0047/2020
HongKong/CUHK2/2020
Wales/PHW06/2020
# Excluding because seem to be too divergent - worth double checking
Shandong/LY002/2020
Shandong/LY001/2020
USA/MN1-MDH1/2020
USA/WA-UW40/2020
USA/WA-UW53/2020
USA/WA-UW65/2020
USA/WA11-UW7/2020
Wuhan/IVDC-HB-envF13/2020
USA/WA-UW48/2020
USA/WA-UW45/2020
France/HF1805/2020
# Bat and pangolin relatives, too divergent to be included here
bat/Yunnan/RaTG13/2013
pangolin/Guandong/1/2020
pangolin/Guangdong/1/2019
pangolin/Guangdong/P2S/2019
pangolin/Guangxi/P1E/2017
pangolin/Guangxi/P2V/2017
pangolin/Guangxi/P3B/2017
pangolin/Guangxi/P4L/2017
pangolin/Guangxi/P5E/2017
pangolin/Guangxi/P5L/2017
pangolin/Guandong/1/2019
pangolin/China/MP789/2019
bat/Yunnan/RmYN02/2019
bat/Yunnan/RmYN01/2019
# Temporarily excluded
USA/CruiseA-1/2020
USA/CruiseA-2/2020
USA/CruiseA-3/2020
USA/CruiseA-4/2020
USA/CruiseA-5/2020
USA/CruiseA-6/2020
USA/CruiseA-7/2020
USA/CruiseA-8/2020
USA/CruiseA-9/2020
USA/CruiseA-10/2020
USA/CruiseA-11/2020
USA/CruiseA-12/2020
USA/CruiseA-13/2020
USA/CruiseA-14/2020
USA/CruiseA-15/2020
USA/CruiseA-16/2020
USA/CruiseA-17/2020
USA/CruiseA-18/2020
USA/CruiseA-19/2020
USA/CruiseA-20/2020
USA/CruiseA-21/2020
USA/CruiseA-22/2020
USA/CruiseA-23/2020
USA/CruiseA-24/2020
USA/CruiseA-25/2020
USA/CruiseA-26/2020
# way too divergent
Russia/StPetersburg-3524/2020
# temporarily excluded because is currently reverse complement
Peru/010/2020
# Japan Diamond Princess sequences
Japan/DP0005/2020
Japan/DP0027/2020
Japan/DP0037/2020
Japan/DP0058/2020
Japan/DP0059/2020
Japan/DP0065/2020
Japan/DP0077/2020
Japan/DP0078/2020
Japan/DP0104/2020
Japan/DP0107/2020
Japan/DP0121/2020
Japan/DP0133/2020
Japan/DP0134/2020
Japan/DP0152/2020
Japan/DP0158/2020
Japan/DP0184/2020
Japan/DP0190/2020
Japan/DP0191/2020
Japan/DP0196/2020
Japan/DP0200/2020
Japan/DP0236/2020
Japan/DP0274/2020
Japan/DP0278/2020
Japan/DP0286/2020
Japan/DP0287/2020
Japan/DP0289/2020
Japan/DP0290/2020
Japan/DP0294/2020
Japan/DP0311/2020
Japan/DP0319/2020
Japan/DP0328/2020
Japan/DP0344/2020
Japan/DP0346/2020
Japan/DP0357/2020
Japan/DP0361/2020
Japan/DP0438/2020
Japan/DP0457/2020
Japan/DP0462/2020
Japan/DP0464/2020
Japan/DP0476/2020
Japan/DP0481/2020
Japan/DP0482/2020
Japan/DP0543/2020
Japan/DP0544/2020
Japan/DP0568/2020
Japan/DP0588/2020
Japan/DP0644/2020
Japan/DP0645/2020
Japan/DP0654/2020
Japan/DP0687/2020
Japan/DP0690/2020
Japan/DP0697/2020
Japan/DP0699/2020
Japan/DP0700/2020
Japan/DP0703/2020
Japan/DP0724/2020
Japan/DP0743/2020
Japan/DP0752/2020
Japan/DP0763/2020
Japan/DP0764/2020
Japan/DP0765/2020
Japan/DP0779/2020
Japan/DP0785/2020
Japan/DP0786/2020
Japan/DP0802/2020
Japan/DP0803/2020
Japan/DP0804/2020
Japan/DP0827/2020
Japan/DP0880/2020
Japan/DP0890/2020