Table 3. Detected polymorphism.
| Polymorphism in the repeat motifc | Polymorphism in the flanking sequencesc | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Species | Number of loci | Number of alleles with sequence differencea | Number of alleles differing by amplicon sizeb | % of size homoplasy | % of increase in alleles due to sequence | Repeat number variation | SNP | Indel | SNP | Indel |
| S. salard | 14 | 122 | 108 | 11% | 13% | 107 (14) | 3 (3) | – | 2 (2) | 3 (3) |
| Quercus sp. | 40 | 537 | 346 | 35% | 55% | 406 (40) | 38 (25) | 1 (1) | 47 (18) | 13 (10) |
| Alosa sp. | 24 | 174 | 150 | 14% | 16% | 130 (23) | 13 (15) | 2 (2) | 4 (4) | 3 (3) |
| A. ostoyae | 38 | 398 | 187 | 53% | 113% | 187 (33) | 79 (26) | 8 (7) | 312 (23) | 41 (16) |
| M. variegatipes | 39 | 166 | 156 | 6% | 6% | 147 (39) | 3 (3) | 1 (1) | 9 (7) | 5 (5) |
Notes.
a
Irrespectively of polymorphism type, computed based on the Combined analysis strategy.
b
Simulating the number of alleles that would have been identified using traditional capillary electrophoresis, computed based on the FullLength analysis strategy and accounting for allele size only on the same locus as the Combined approach.
c
Total number of alleles (and number of loci in brackets) for each polymorphism type.
d
Combination of two sequence based microsatellite genotyping protocols.