Table 1 Combinations of parameters used in the optimization of phenetic clustering of SARS-CoV-2 genomes.
From: HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Freq. Threshold | Pers. Threshold | VOC > 1HG/Tot VOC | VOC > 1HG/ Tot VOI | VUM > 1HG/Tot VUM | Tot HGs |
|---|---|---|---|---|---|
0.5 | 10 | 5/5 | 9/9 | 14/14 | 7936 |
0.5 | 15 | 5/5 | 9/9 | 14/14 | 5854 |
0.5 | 25 | 5/5 | 9/9 | 14/14 | 4799 |
0.5 | 50 | 4/5 | 8/9 | 10/14 | 4076 |
0.5 | 75 | 3/5 | 7/9 | 9/14 | 3960 |
0.5 | 100 | 2/5 | 4/9 | 8/14 | 2957 |
1 | 10 | 5/5 | 9/9 | 14/14 | 2979 |
1 | 15 | 5/5 | 9/9 | 14/14 | 1571 |
1 | 25 | 5/5 | 9/9 | 13/14 | 976 |
1 | 50 | 5/5 | 8/9 | 13/14 | 863 |
1 | 75 | 4/5 | 7/9 | 11/14 | 801 |
1 | 100 | 2/5 | 5/9 | 8/14 | 736 |
2.5 | 10 | 5/5 | 8/9 | 11/14 | 1360 |
2.5 | 15 | 5/5 | 7/9 | 10/14 | 1182 |
2.5 | 25 | 5/5 | 7/9 | 10/14 | 938 |
2.5 | 50 | 2/5 | 6/9 | 10/14 | 801 |
2.5 | 75 | 2/5 | 5/9 | 4/14 | 736 |
2.5 | 100 | 2/5 | 4/9 | 4/14 | 583 |
5 | 10 | 5/5 | 7/9 | 6/14 | 768 |
5 | 15 | 2/5 | 4/9 | 6/14 | 659 |
5 | 25 | 2/5 | 3/9 | 4/14 | 482 |
5 | 50 | 1/5 | 2/9 | 4/14 | 424 |
5 | 75 | 1/5 | 1/9 | 2/14 | 401 |
5 | 100 | 1/5 | 1/9 | 2/14 | 388 |
