Table 1.
Number of SNPs in 43 T. gondii type II whole genomes compared to a ME49 genome (ToxoDB release 47) in non-overlapping windows of 333 bp of the genome. Four prioritization categories of target regions for the new Ion AmpliSeq-based typing method were defined based on the number of SNPs
| Chromosome | Number of SNPs relative to ME49 in 43 T. gondii type II whole genomes per 333 bp windows | Total | SNPs/10 kb | ||||
|---|---|---|---|---|---|---|---|
| 1–4 | 5-9 (4th priority targets) | 10-14 (3rd priority targets) | 15-19 (2nd priority targets) | 20-35 (1st priority targets) | |||
| Ia | 1158 | 11 | 3 | 0 | 0 | 1172 | 6.30 |
| Ib | 1643 | 20 | 4 | 1 | 0 | 1668 | 8.53 |
| II | 1717 | 38 | 9 | 3 | 0 | 1767 | 7.53 |
| III | 1962 | 50 | 19 | 5 | 0 | 2036 | 8.04 |
| IV | 2145 | 35 | 8 | 1 | 1 | 2190 | 8.15 |
| V | 2677 | 68 | 29 | 11 | 9 | 2543 | 6.95 |
| VI | 2508 | 28 | 5 | 0 | 2 | 3858 | 8.49 |
| VIIa | 3784 | 60 | 6 | 4 | 4 | 3821 | 7.54 |
| VIIb | 3783 | 35 | 3 | 0 | 0 | 5543 | 7.95 |
| VIII | 5491 | 41 | 9 | 2 | 0 | 4803 | 7.59 |
| IX | 4704 | 77 | 18 | 3 | 1 | 2794 | 8.39 |
| X | 5622 | 132 | 15 | 6 | 1 | 5776 | 7.72 |
| XI | 4729 | 41 | 5 | 0 | 1 | 4776 | 7.21 |
| XII | 4804 | 37 | 3 | 1 | 0 | 4845 | 6.83 |
| Total | 46,727 | 673 | 136 | 37 | 19 | 47,592 | 8.00 |