Table 5.
The Number of Loci (and SNPs) Obtained from Different Assemblies of the ddRADseq Data
| Minimum Individualsa |
||||||||
|---|---|---|---|---|---|---|---|---|
| 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | |
| 95% clusteringb, paralog = 1c | 1,079 (2,228) | 375 (841) | 173 (404) | 72 (182) | 27 (73) | 9 (26) | 3 (7) | 0 (0) |
| 95% clustering, paralog = 3 | 1,100 (2,282) | 384 (860) | 177 (413) | 74 (186) | 28 (76) | 10 (29) | 3 (7) | 0 (0) |
| 90% clustering, paralog = 1 | 1,826 (6,506) | 674 (2,637) | 306 (1,212) | 154 (632) | 68 (306) | 28 (128) | 7 (27) | 1 (3) |
| 90% clustering, paralog = 3 | 1,856 (6,655) | 693 (2,733) | 312 (1,244) | 158 (655) | 69 (313) | 29 (135) | 8 (34) | 1 (3) |
| 80% clustering, paralog = 1 | 2,629 (15,725) | 1,057 (6,893) | 478 (3,037) | 227 (1,409) | 109 (722) | 50 (348) | 13 (75) | 2 (13) |
| 80% clustering, paralog = 3 | 2,670 (16,002) | 1,083 (7,079) | 493 (3,155) | 234 (1,458) | 113 (752) | 53 (371) | 13 (75) | 2 (13) |
aMinimum number of individuals (min. ind.) required to retain a locus in the final alignment (out of ten sequences total).
bThreshold for both within-sample and across-sample clustering.
cMaximum number of shared polymorphic bases.