Table 3.
List of homozygous SNPs located within the coding region. Position of the SNP and CDS coordinates refer to the virulent strain
| contig (virulent strain) | SNP position | CDS start | CDS end | CDS strand | gene ID virulent strain | gene ID attenuated strain | functional annotation | SNP type | PROVEAN prediction (threshold ≤ −2.5) |
|---|---|---|---|---|---|---|---|---|---|
| contig_1 | 808,350 | 807,890 | 809,134 | – | g222 | g1540 | Clan MG, family M24, aminopeptidase P-like metallopeptidase | non synonymous missense T262R | neutral (score − 0.566) |
| contig_4 | 907,239 | 906,962 | 907,699 | + | g6022 | g2624 | unknown; domain superfamily: PRK05901-RNA polymerase sigma factor, provisional | non synonymous missense D93V | deleterious |
| contig_9 | 56,933 | 56,370 | 59,399 | + | g9263 | g1249 | Rho-GEF | non synonymous missense M188I | neutral (score 1.600) |
| contig_9 | 754,604 | 754,419 | 755,309 | – | g9462 | g9315 | Ser/Thr protein phosphatase | non synonymous missense F236V | neutral (score 0.252) |
| contig_24 | 8498 | 8153 | 9325 | + | g3899 | g1904 | guanidine-nucleotide exchange factor domain containing protein | non synonymous missense P116S | neutral (score 0.717) |
| contig_24 | 135,940 | 135,268 | 135,959 | + | g3944 | g1860 | CAMK family serine/threonine-protein kinase 25-like | non synonymous missense M258K | deleterious (score − 2906.0) |
| contig_30 | 608,903 | 608,341 | 611,167 | + | g4054 | g10480 | alpha amylase domain-containing protein | non synonymous missense S188F | neutral (score − 0.233) |
| contig_39 | 136,516 | 136,175 | 136,771 | + | g5742 | g4148 | transposable element Tcb2 transposase | synonymous | n.d.* |
| contig_46 | 126,968 | 124,401 | 127,370 | – | g6691 | g4310 | BspA family leucine-rich repeat surface protein | non synonymous missense E135K | neutral (score 0.067) |
| contig_51 | 970,026 | 967,493 | 970,771 | + | g7214 | g10757 | Major Facilitator Superfamily transporter | non synonymous missense K845M | neutral (score − 1.744) |
| contig_55 | 233,376 | 232,271 | 233,587 | + | g7655 | g5929 | Myb-like DNA-binding domain containing protein | non synonymous missense R369M | neutral (score − 0.712) |
| contig_68 | 549,886 | 546,983 | 550,105 | + | g8542 | g6202 | unknown | synonymous | n.d. |
| contig_68 | 639,193 | 639,152 | 640,081 | – | g8565 | g6179 | hypothetical protein | non synonymous missense M297L | neutral (score − 1.0) |
| contig_72 | 57,296 | 56,499 | 58,331 | + | g8794 | g337 | leucine rich repeat containing protein | non synonymous nonsense W266del | deleterious (score − 56.252) |
| contig_82 | 121,399 | 120,392 | 121,525 | + | g9013 | g1396 | type IIB DNA topoisomerase family protein | synonymous | n.d. |
| contig_118 | 307,118 | 306,262 | 307,380 | – | g931 | g3679 | POC1 centriolar protein homolog B | non synonymous missense P88R | neutral (score 0.655) |
| scaffold_61 | 3,064,020 | 3,064,015 | 3,066,186 | + | G10965 | G6535 | chitinase-like protein | synonymous | n.d. |
*n.d. not done