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updated allele databases #76

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Apr 26, 2024
Merged

updated allele databases #76

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194 changes: 100 additions & 94 deletions kleborate/data/AbST_profiles.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,94 +1,100 @@
ST iucA iucB iucC iucD iutA iuc_lineage
1 1 1 1 1 1 iuc 1
2 2 6 13 6 46 iuc 2
3 2 6 13 6 26 iuc 2
4 5 4 3 11 6 iuc 2A
5 1 1 1 1 10 iuc 1
6 2 6 5 15 8 iuc 2
7 5 4 16 11 6 iuc 2A
8 1 1 1 1 50 iuc 1
9 1 1 1 1 7 iuc 1
10 11 4 9 3 12 iuc 2A
11 7 2 2 2 2 iuc 2
12 8 1 1 1 1 iuc 1
13 9 7 7 8 9 iuc 3
14 2 2 2 2 2 iuc 2
15 1 1 1 7 1 iuc 1
16 1 3 1 1 1 iuc 1
17 6 1 6 1 1 iuc 1
18 21 1 1 19 1 iuc 1
19 10 1 8 9 11 iuc 1
20 1 1 1 1 3 iuc 1
21 1 19 1 1 1 iuc 1
22 1 1 29 1 10 iuc 1
23 14 9 12 12 16 iuc 3
24 2 6 5 6 8 iuc 2
25 9 7 12 8 17 iuc 3
26 1 1 20 1 49 iuc 1
27 1 1 1 18 1 iuc 1
28 20 1 1 1 1 iuc 1
29 3 4 3 3 4 iuc 2A
30 4 5 4 4 5 iuc 4
31 2 10 14 2 26 iuc 2
32 9 11 12 8 17 iuc 3
33 1 1 1 1 47 iuc 1
34 1 1 1 16 1 iuc 1
35 1 1 17 1 1 iuc 1
36 39 1 1 1 1 iuc 1
37 1 1 31 1 1 iuc 1
38 2 2 2 17 2 iuc 2
39 5 4 3 5 6 iuc 2A
40 24 4 3 20 6 iuc 2A
41 12 14 22 21 51 iuc 3
42 12 14 22 22 13 iuc 3
43 25 9 25 23 52 iuc 3
44 4 5 26 4 5 iuc 4
45 28 4 3 11 54 iuc 2A
46 5 4 3 27 6 iuc 2A
47 5 16 3 11 6 iuc 2A
48 34 18 11 28 6 iuc 2A
49 25 9 30 31 52 iuc 3
50 43 20 3 32 6 iuc 2A
51 5 4 27 11 6 iuc 2A
52 26 5 4 24 5 iuc 4
53 27 4 27 25 53 iuc 2A
54 30 4 3 3 12 iuc 2A
55 31 4 3 3 12 iuc 2A
56 35 4 3 20 6 iuc 2A
57 27 4 3 20 6 iuc 2A
58 37 5 4 4 56 iuc 4
59 45 22 33 35 48 iuc 5
60 45 12 33 35 60 iuc 5
61 45 24 33 35 61 iuc 5
62 45 12 33 35 61 iuc 5
63 1 15 1 1 1 iuc 1
64 9 7 12 13 17 iuc 3
65 1 1 15 1 1 iuc 1
66 45 21 33 39 24 iuc 5
67 51 1 39 1 37 iuc 1
68 51 1 40 1 38 iuc 1
69 12 29 42 34 13 iuc 3
70 9 33 12 8 34 iuc 3
71 12 14 42 38 30 iuc 3
72 12 30 22 37 33 iuc 3
73 12 30 22 37 31 iuc 3
74 12 30 22 37 32 iuc 3
75 1 1 1 1 36 iuc 1
76 1 1 41 1 1 iuc 1
77 1 1 1 33 1 iuc 1
78 1 1 34 1 1 iuc 1
79 9 34 38 8 9 iuc 3
80 9 7 12 8 35 iuc 3
81 9 35 12 8 17 iuc 3
83 9 33 12 8 17 iuc 3
84 53 2 13 2 26 iuc 2
85 12 14 22 36 51 iuc 3
86 12 30 22 37 13 iuc 3
87 12 31 22 37 13 iuc 3
88 25 9 25 31 52 iuc 3
89 25 9 45 23 52 iuc 3
90 25 9 43 23 39 iuc 3
91 25 9 25 31 40 iuc 3
92 25 36 25 31 52 iuc 3
93 25 9 44 31 52 iuc 3
94 45 12 33 35 22 iuc 5
ST iucA iucB iucC iucD iutA iuc_lineage
1 1 1 1 1 1 iuc 1
2 2 6 13 6 46 iuc 2
3 2 6 13 6 26 iuc 2
4 5 4 3 11 6 iuc 2A
5 1 1 1 1 10 iuc 1
6 2 6 5 15 8 iuc 2
7 5 4 16 11 6 iuc 2A
8 1 1 1 1 50 iuc 1
9 1 1 1 1 7 iuc 1
10 11 4 9 3 12 iuc 2A
11 7 2 2 2 2 iuc 2
12 8 1 1 1 1 iuc 1
13 9 7 7 8 9 iuc 3
14 2 2 2 2 2 iuc 2
15 1 1 1 7 1 iuc 1
16 1 3 1 1 1 iuc 1
17 6 1 6 1 1 iuc 1
18 21 1 1 19 1 iuc 1
19 10 1 8 9 11 iuc 1
20 1 1 1 1 3 iuc 1
21 1 19 1 1 1 iuc 1
22 1 1 29 1 10 iuc 1
23 14 9 12 12 16 iuc 3
24 2 6 5 6 8 iuc 2
25 9 7 12 8 17 iuc 3
26 1 1 20 1 49 iuc 1
27 1 1 1 18 1 iuc 1
28 20 1 1 1 1 iuc 1
29 3 4 3 3 4 iuc 2A
30 4 5 4 4 5 iuc 4
31 2 10 14 2 26 iuc 2
32 9 11 12 8 17 iuc 3
33 1 1 1 1 47 iuc 1
34 1 1 1 16 1 iuc 1
35 1 1 17 1 1 iuc 1
36 39 1 1 1 1 iuc 1
37 1 1 31 1 1 iuc 1
38 2 2 2 17 2 iuc 2
39 5 4 3 5 6 iuc 2A
40 24 4 3 20 6 iuc 2A
41 12 14 22 21 51 iuc 3
42 12 14 22 22 13 iuc 3
43 25 9 25 23 52 iuc 3
44 4 5 26 4 5 iuc 4
45 28 4 3 11 54 iuc 2A
46 5 4 3 27 6 iuc 2A
47 5 16 3 11 6 iuc 2A
48 34 18 11 28 6 iuc 2A
49 25 9 30 31 52 iuc 3
50 43 20 3 32 6 iuc 2A
51 5 4 27 11 6 iuc 2A
52 26 5 4 24 5 iuc 4
53 27 4 27 25 53 iuc 2A
54 30 4 3 3 12 iuc 2A
55 31 4 3 3 12 iuc 2A
56 35 4 3 20 6 iuc 2A
57 27 4 3 20 6 iuc 2A
58 37 5 4 4 56 iuc 4
59 45 22 33 35 48 iuc 5
60 45 12 33 35 60 iuc 5
61 45 24 33 35 61 iuc 5
62 45 12 33 35 61 iuc 5
63 1 15 1 1 1 iuc 1
64 9 7 12 13 17 iuc 3
65 1 1 15 1 1 iuc 1
66 45 21 33 39 24 iuc 5
67 51 1 39 1 37 iuc 1
68 51 1 40 1 38 iuc 1
69 12 29 42 34 13 iuc 3
70 9 33 12 8 34 iuc 3
71 12 14 42 38 30 iuc 3
72 12 30 22 37 33 iuc 3
73 12 30 22 37 31 iuc 3
74 12 30 22 37 32 iuc 3
75 1 1 1 1 36 iuc 1
76 1 1 41 1 1 iuc 1
77 1 1 1 33 1 iuc 1
78 1 1 34 1 1 iuc 1
79 9 34 38 8 9 iuc 3
80 9 7 12 8 35 iuc 3
81 9 35 12 8 17 iuc 3
83 9 33 12 8 17 iuc 3
84 53 2 13 2 26 iuc 2
85 12 14 22 36 51 iuc 3
86 12 30 22 37 13 iuc 3
87 12 31 22 37 13 iuc 3
88 25 9 25 31 52 iuc 3
89 25 9 45 23 52 iuc 3
90 25 9 43 23 39 iuc 3
91 25 9 25 31 40 iuc 3
92 25 36 25 31 52 iuc 3
93 25 9 44 31 52 iuc 3
94 45 12 33 35 22 iuc 5
95 46 1 1 1 1 iuc 1
96 25 9 25 23 80 iuc 3
97 56 7 12 8 9 iuc 3
98 57 7 12 8 35 iuc 3
99 58 9 25 31 52 iuc 3
100 25 9 25 23 39 iuc 3
161 changes: 83 additions & 78 deletions kleborate/data/CbST_profiles.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,78 +1,83 @@
ST clbA clbB clbC clbD clbE clbF clbG clbH clbI clbL clbM clbN clbO clbP clbQ clb_lineage
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
2 1 13 1 1 1 3 5 6 6 1 1 1 4 1 1 clb 1
3 1 13 1 1 1 3 5 6 6 1 1 12 4 1 1 clb 1
4 1 13 1 1 1 3 5 6 9 1 1 1 4 1 1 clb 1
5 1 14 1 1 1 3 1 9 7 1 1 1 3 5 3 clb 1
6 1 15 6 5 1 3 5 6 8 1 1 1 5 1 1 clb 1
7 1 19 1 1 1 3 6 6 3 1 1 1 11 1 1 clb 1
8 1 26 1 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
9 1 4 1 1 1 1 1 5 1 1 1 1 1 1 1 clb 1
10 1 5 4 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
11 1 5 4 1 1 1 3 1 1 1 3 4 1 1 1 clb 1
12 2 10 10 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
13 2 10 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 3
14 2 2 2 2 6 2 2 3 2 2 2 2 2 2 2 clb 2
15 2 10 2 2 2 2 2 3 2 2 2 2 6 2 2 clb 3
16 2 10 2 2 2 2 2 3 2 2 2 9 2 9 2 clb 3
17 2 10 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
18 2 10 2 2 2 4 2 10 2 2 2 2 2 2 2 clb 3
19 2 10 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
20 2 10 2 2 2 4 2 8 2 2 2 2 2 8 2 clb 3
21 2 10 2 2 2 4 2 8 2 2 2 22 2 2 2 clb 3
22 2 16 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
23 2 17 2 2 2 2 2 8 2 2 5 2 2 2 2 clb 3
24 2 18 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
25 2 2 11 2 2 2 2 3 2 6 2 2 2 2 2 clb 2
26 2 2 2 2 2 2 2 3 2 2 2 14 2 2 2 clb 2
27 2 2 2 2 2 2 2 3 2 2 2 2 17 2 2 clb 2
28 2 2 2 2 2 2 2 3 2 2 2 2 18 2 2 clb 2
29 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
30 2 2 2 2 2 2 2 3 2 2 2 2 2 6 2 clb 2
31 2 2 2 2 2 2 2 3 2 2 2 2 2 7 2 clb 2
32 2 2 2 2 2 2 2 3 2 2 2 3 2 2 2 clb 2
33 2 2 2 2 2 2 2 3 2 7 2 2 2 2 2 clb 2
34 2 2 2 2 2 2 2 3 2 8 2 2 2 2 2 clb 2
35 2 2 2 2 7 2 2 3 2 2 2 2 2 2 2 clb 2
36 2 2 2 6 2 2 2 3 2 2 2 2 2 2 2 clb 2
37 2 2 5 2 4 2 2 3 2 2 4 2 2 2 2 clb 2
38 2 24 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
39 2 25 2 7 2 2 2 16 2 5 2 10 2 2 2 clb 2
40 2 27 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
41 2 28 2 2 2 10 2 3 2 2 2 2 2 2 2 clb 2
42 2 29 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
43 2 30 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
44 2 32 2 2 2 2 2 3 2 2 2 2 2 4 2 clb 2
45 2 36 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
46 2 37 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
47 2 38 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
48 2 39 2 2 2 11 2 8 2 2 2 2 2 2 2 clb 3
49 2 39 2 2 2 2 2 18 2 2 2 2 2 2 2 clb 3
50 2 39 2 2 2 2 2 20 2 2 2 2 2 2 2 clb 3
51 2 39 2 2 2 2 2 8 13 2 2 2 2 2 2 clb 3
52 2 39 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
53 2 43 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
54 2 8 2 2 3 2 2 7 2 2 2 2 2 2 2 clb 3
55 2 9 2 2 2 2 2 8 4 2 2 2 2 2 2 clb 3
56 4 33 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
57 4 34 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
58 4 35 1 3 1 3 1 19 3 1 1 8 14 1 1 clb 1
59 4 6 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
60 5 10 2 2 2 4 2 8 11 2 2 2 2 2 2 clb 3
61 5 10 2 2 2 4 2 8 12 2 2 2 2 2 2 clb 3
62 5 10 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
63 5 21 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
64 6 10 2 2 2 2 2 17 2 2 2 2 2 2 2 clb 3
65 7 6 1 3 1 3 1 6 3 1 8 16 14 1 1 clb 1
66 1 65 1 1 1 3 1 25 3 1 1 1 14 1 1 clb 1
67 1 15 6 1 1 3 5 6 3 1 1 24 5 1 1 clb 1
68 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 clb 2
69 8 10 21 2 2 2 2 28 2 2 2 2 2 2 2 clb 3
70 1 66 1 1 9 3 1 6 23 1 1 25 16 1 1 clb 1
71 2 68 2 2 2 2 2 2 2 2 2 2 2 2 2 clb 2
72 9 2 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
73 2 10 21 2 2 2 2 28 2 2 2 2 2 2 2 clb 3
74 1 67 1 1 1 3 10 25 3 1 1 26 14 1 1 clb 1
75 1 13 1 1 1 3 5 6 6 1 1 27 4 1 1 clb 1
76 1 7 1 1 1 3 1 6 3 1 1 1 3 12 1 clb 1
77 2 69 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
ST clbA clbB clbC clbD clbE clbF clbG clbH clbI clbL clbM clbN clbO clbP clbQ clb_lineage
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
2 1 13 1 1 1 3 5 6 6 1 1 1 4 1 1 clb 1
3 1 13 1 1 1 3 5 6 6 1 1 12 4 1 1 clb 1
4 1 13 1 1 1 3 5 6 9 1 1 1 4 1 1 clb 1
5 1 14 1 1 1 3 1 9 7 1 1 1 3 5 3 clb 1
6 1 15 6 5 1 3 5 6 8 1 1 1 5 1 1 clb 1
7 1 19 1 1 1 3 6 6 3 1 1 1 11 1 1 clb 1
8 1 26 1 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
9 1 4 1 1 1 1 1 5 1 1 1 1 1 1 1 clb 1
10 1 5 4 1 1 1 1 1 1 1 1 1 1 1 1 clb 1
11 1 5 4 1 1 1 3 1 1 1 3 4 1 1 1 clb 1
12 2 10 10 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
13 2 10 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 3
14 2 2 2 2 6 2 2 3 2 2 2 2 2 2 2 clb 2
15 2 10 2 2 2 2 2 3 2 2 2 2 6 2 2 clb 3
16 2 10 2 2 2 2 2 3 2 2 2 9 2 9 2 clb 3
17 2 10 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
18 2 10 2 2 2 4 2 10 2 2 2 2 2 2 2 clb 3
19 2 10 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
20 2 10 2 2 2 4 2 8 2 2 2 2 2 8 2 clb 3
21 2 10 2 2 2 4 2 8 2 2 2 22 2 2 2 clb 3
22 2 16 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
23 2 17 2 2 2 2 2 8 2 2 5 2 2 2 2 clb 3
24 2 18 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
25 2 2 11 2 2 2 2 3 2 6 2 2 2 2 2 clb 2
26 2 2 2 2 2 2 2 3 2 2 2 14 2 2 2 clb 2
27 2 2 2 2 2 2 2 3 2 2 2 2 17 2 2 clb 2
28 2 2 2 2 2 2 2 3 2 2 2 2 18 2 2 clb 2
29 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
30 2 2 2 2 2 2 2 3 2 2 2 2 2 6 2 clb 2
31 2 2 2 2 2 2 2 3 2 2 2 2 2 7 2 clb 2
32 2 2 2 2 2 2 2 3 2 2 2 3 2 2 2 clb 2
33 2 2 2 2 2 2 2 3 2 7 2 2 2 2 2 clb 2
34 2 2 2 2 2 2 2 3 2 8 2 2 2 2 2 clb 2
35 2 2 2 2 7 2 2 3 2 2 2 2 2 2 2 clb 2
36 2 2 2 6 2 2 2 3 2 2 2 2 2 2 2 clb 2
37 2 2 5 2 4 2 2 3 2 2 4 2 2 2 2 clb 2
38 2 24 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
39 2 25 2 7 2 2 2 16 2 5 2 10 2 2 2 clb 2
40 2 27 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
41 2 28 2 2 2 10 2 3 2 2 2 2 2 2 2 clb 2
42 2 29 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
43 2 30 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
44 2 32 2 2 2 2 2 3 2 2 2 2 2 4 2 clb 2
45 2 36 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
46 2 37 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
47 2 38 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
48 2 39 2 2 2 11 2 8 2 2 2 2 2 2 2 clb 3
49 2 39 2 2 2 2 2 18 2 2 2 2 2 2 2 clb 3
50 2 39 2 2 2 2 2 20 2 2 2 2 2 2 2 clb 3
51 2 39 2 2 2 2 2 8 13 2 2 2 2 2 2 clb 3
52 2 39 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
53 2 43 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
54 2 8 2 2 3 2 2 7 2 2 2 2 2 2 2 clb 3
55 2 9 2 2 2 2 2 8 4 2 2 2 2 2 2 clb 3
56 4 33 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
57 4 34 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
58 4 35 1 3 1 3 1 19 3 1 1 8 14 1 1 clb 1
59 4 6 1 3 1 3 1 6 3 1 1 8 14 1 1 clb 1
60 5 10 2 2 2 4 2 8 11 2 2 2 2 2 2 clb 3
61 5 10 2 2 2 4 2 8 12 2 2 2 2 2 2 clb 3
62 5 10 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
63 5 21 2 2 2 4 2 8 2 2 2 2 2 2 2 clb 3
64 6 10 2 2 2 2 2 17 2 2 2 2 2 2 2 clb 3
65 7 6 1 3 1 3 1 6 3 1 8 16 14 1 1 clb 1
66 1 65 1 1 1 3 1 25 3 1 1 1 14 1 1 clb 1
67 1 15 6 1 1 3 5 6 3 1 1 24 5 1 1 clb 1
68 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 clb 2
69 8 10 21 2 2 2 2 28 2 2 2 2 2 2 2 clb 3
70 1 66 1 1 9 3 1 6 23 1 1 25 16 1 1 clb 1
71 2 68 2 2 2 2 2 2 2 2 2 2 2 2 2 clb 2
72 9 2 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
73 2 10 21 2 2 2 2 28 2 2 2 2 2 2 2 clb 3
74 1 67 1 1 1 3 10 25 3 1 1 26 14 1 1 clb 1
75 1 13 1 1 1 3 5 6 6 1 1 27 4 1 1 clb 1
76 1 7 1 1 1 3 1 6 3 1 1 1 3 12 1 clb 1
77 2 69 2 2 2 2 2 3 2 2 2 2 2 2 2 clb 2
78 2 2 2 2 2 2 2 3 2 2 2 2 2 13 2 clb 2
79 2 53 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
80 2 71 2 2 2 2 2 8 2 2 2 2 2 2 2 clb 3
81 2 53 2 2 2 2 2 8 2 2 2 2 2 14 2 clb 3
82 2 53 2 2 2 2 2 8 2 2 2 28 2 2 2 clb 3
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