Table 1.
General description of standard SPInDel profiles on eukaryotic, prokaryotic and viral groups
| Taxonomic group | Number of reference sequences (N) | Number of conserved regions | Number of hypervariable regions (n) | Average number of pairwise differences ( ) |
Average number of pairwise differences per hypervariable region | Number of species-specific profiles (Nsp) | Frequency of species-specific profiles (fnG) | Number of species with species-shared profiles | Number of species-shared profiles (Nsh) (number of species with shared profiles) |
||
|---|---|---|---|---|---|---|---|---|---|---|---|
| From different genera | From the same genus | Between subspecies or hybrids | |||||||||
| Eukaryotes | |||||||||||
| Viridiplantae (Vi) | 23 | 9 | 8 | 6.51 | 0.81 | 19 | 0.83 | 4 | 0 | 0 | 2 (4) |
| Stramenopiles (St) | 14 | 11 | 10 | 7.71 | 0.77 | 14 | 1.00 | 0 | 0 | 0 | 0 |
| Fungi (Fu) | 42 | 7 | 6 | 5.90 | 0.98 | 40 | 0.95 | 2 | 0 | 1 (2) | 0 |
| Alveolata (Al) | 6 | 8 | 7 | 4.67 | 0.67 | 6 | 1.00 | 0 | 0 | 0 | 0 |
| Porifera (Po) | 20 | 10 | 9 | 8.65 | 0.96 | 20 | 1.00 | 0 | 0 | 0 | 0 |
| Cnidaria (Cn) | 32 | 8 | 7 | 5.64 | 0.81 | 27 | 0.84 | 5 | 0 | 2 (5) | 0 |
| Platyhelminthes (Pl) | 29 | 10 | 9 | 7.93 | 0.88 | 29 | 1.00 | 0 | 0 | 0 | 0 |
| Echinodermata (Ec) | 20 | 6 | 5 | 3.91 | 0.78 | 18 | 0.90 | 2 | 0 | 1 (2) | 0 |
| Nematoda (Ne) | 29 | 6 | 5 | 4.00 | 0.80 | 27 | 0.93 | 2 | 0 | 1 (2) | 0 |
| Arthropoda (Ar) | 204 | 6 | 5 | 4.72 | 0.94 | 196 | 0.96 | 8 | 0 | 4 (8) | 0 |
| Mollusca (Mo) | 50 | 6 | 5 | 4.17 | 0.83 | 48 | 0.96 | 2 | 0 | 1 (2) | 0 |
| Actinopterygii (Ac) | 539 | 11 | 10 | 7.48 | 0.75 | 492 | 0.91 | 47 | 7 (14) | 10 (31) | 1 (2) |
| Amphibia (Am) | 84 | 7 | 6 | 5.12 | 0.85 | 81 | 0.96 | 3 | 0 | 1 (3) | 0 |
| Testudines (Te) | 29 | 11 | 10 | 7.74 | 0.77 | 29 | 1.00 | 0 | 0 | 0 | 0 |
| Lepidosauria (Le) | 69 | 8 | 7 | 5.36 | 0.77 | 69 | 1.00 | 0 | 0 | 0 | 0 |
| Aves (Av) | 98 | 12 | 11 | 8.90 | 0.81 | 94 | 0.96 | 4 | 0 | 0 | 1 (4) |
| Metatheria (Me) | 31 | 13 | 12 | 8.95 | 0.75 | 31 | 1.00 | 0 | 0 | 0 | 0 |
| Eutheria (Eu) | 237 | 13 | 12 | 9.63 | 0.80 | 211 | 0.89 | 26 | 3 (10) | 3 (7) | 4 (9) |
| Total [percentage of species from total N] | 1556 | 1451 [93.3%] | (Mean: 0.95) | 105 [6.75%] | 10 (24) [1.54%] | 24 (62) [3.98%] | 8 (19) [1.22%] | ||||
| Intra-species data sets | Number of species-shared profiles (Nsh) | ||||||||||
| Caenorhabditis briggsae | 25 | 6 | 5 | 0.08 | 0.02 | 1 | 0.04 | 24 | 1 | ||
| Drosophila simulans | 28 | 6 | 5 | 1.40 | 0.28 | 0 | 0 | 28 | 5 | ||
| Bos taurus | 145 | 13 | 12 | 0.51 | 0.04 | 3 | 0.02 | 142 | 6 | ||
| Homo sapiens | 5664 | 13 | 12 | 0.43 | 0.04 | 10 | 0.002 | 5654 | 18 | ||
| Prokaryotes | |||||||||||
| Crenarchaeota (Archaea) | 48 | 8 | 7 | 3.60 | 0.51 | 30 | 0.62 | 18 | 6 | ||
| Tenericutes (Bacteria) | 57 | 8 | 7 | 3.78 | 0.54 | 25 | 0.44 | 32 | 10 | ||
| Viruses | |||||||||||
| Lentivirus (Retroviridae) | 11 | 6 | 5 | 3.65 | 0.73 | 4 | 0.36 | 7 | 3 | ||
| Papillomaviridae (dsDNA viruses) | 94 | 6 | 5 | 3.68 | 0.74 | 75 | 0.80 | 19 | 9 | ||
| Rhabdoviridae (ssRNA viruses) | 25 | 6 | 5 | 3.38 | 0.68 | 10 | 0.40 | 15 | 6 | ||