Table 3. Genes within virulence QTL regions, excluding genes with no sequence variation or with synonymous SNP only. No sequence variation other than SNP (e.g., indels) was detected in these genes.
| Locus | Gene description | Number of non-synonymous SNP a | Other SNP b |
| Chromosome II | |||
| ANID_03982 | conserved hypothetical protein (calcineurin-like phosphoesterase)c | 2 conservative | 0 |
| ANID_03985 | MFS transporter | 2 radicald | 0 |
| ANID_03988 | conserved hypothetical protein | 2 conservative, 3 radical | 1 intronic |
| ANID_03995 | delta-aminolevulinic acid dehydratase | 0 | 1 intronic |
| ANID_03998 | conserved hypothetical protein | 2 conservative, 2 radical | 1 upstream, 3 downstream |
| ANID_04005 | conserved hypothetical protein | 4 conservative, 2 radical | 2 intronic, 3 downstream |
| ANID_04006 | conserved hypothetical protein (GMC oxidoreductase)c | 6 conservative | 1 upstream, 4 intronic |
| Chromosome VI | |||
| ANID_03176 | ATP-dependent rRNA helicase spb4 | 0 | 1 intronic |
| ANID_03178 | deacetylase complex subunit Sds3 | 1 conservative | 0 |
| ANID_03179 | conserved hypothetical protein | 1 radical | 0 |
| ANID_03184 | aldose 1-epimerase | 0 | 1 downstream |
| ANID_03186 | conserved hypothetical protein (XPG-I and XPG-N terminal domains)c | 1 conservative | 0 |
| ANID_03193 | conserved hypothetical protein | 0 | 1 UTR |
| ANID_03196 | glycosyl hydrolase family 88 protein | 0 | 1 downstream |
| ANID_03200 | glycoside hydrolase family 2 protein | 1 conservative, 1 radical | 1 upstream,1 intronic, 3 UTR, 1 downstream |
| ANID_03201 | beta-galactosidase | 3 conservative, 1 radical | 2 upstream, 2 downstream |
| ANID_03204 | MFS alpha-glucoside transporter | 1 radical | 0 |
| ANID_03205 | aldehyde dehydrogenase | 3 conservative | 1 upstream, 2 intronic,1 downstream |
| ANID_03209 | high affinity copper transporter | 1 conservative | 0 |
| ANID_10380 | dicer-like protein 2 | 1 radical | 0 |
| ANID_10383 | conserved hypothetical protein (glycosyl hydrolase family 2, sugar binding domain)c | 0 | 1 upstream |
| ANID_10384 | C6 transcription factor | 0 | 1 downstream |
| ANID_12377 | conserved hypothetical protein | 1 radical | 0 |
| Chromosome VII | |||
| ANID_08919 | cytochrome P450 monooxygenase | 1 conservative, 1 radical | 1 intronic |
| ANID_08920 | cytochrome b5 | 0 | 1 downstream |
| ANID_08921 | Dehydrogenase | 0 | 1 intronic, 1 downstream |
| ANID_08923 | conserved hypothetical protein (heterokaryon incompatibility protein)c | 0 | 1 intronic |
| ANID_08925 | conserved hypothetical protein | 1 radical | 1 upstream |
| ANID_08926 | conserved hypothetical protein | 0 | 2 intronic |
| ANID_08928 | ABC multidrug transporter | 1 radical | 0 |
| ANID_08931 | conserved hypothetical protein | 0 | 1 upstream |
| ANID_08932 | TIM-barrel enzyme family protein | 0 | 1 upstream, 2 downstream |
| ANID_08933 | conserved hypothetical protein | 0 | 1 intronic |
| ANID_08937 | 3-oxoacyl-(acyl-carrier-protein) reductase 2 | 1 conservative | 0 |
| ANID_08940 | conserved hypothetical protein | 1 radical | 0 |
| ANID_08941 | Na/K ATPase alpha 1 isoform | 0 | 1 intronic |
| ANID_08945 | TAM domain methyltransferase | 0 | 1 intronic |
| ANID_08951 | conserved hypothetical protein | 0 | ?e |
| ANID_08953 | alpha-glucosidase B | 1 conservative | 0 |
| ANID_08957 | multidrug resistance-associated protein | 2 conservative, 1 radical | 0 |
| ANID_08958 | conserved hypothetical protein | 1 radicalf | 0 |
| ANID_08962 | conserved hypothetical protein | ?e | 0 |
| ANID_08968 | isoflavone reductase | 1 conservative | 0 |
| ANID_08970 | conserved hypothetical protein | 1 conservative | 0 |
| ANID_08971 | integral membrane protein | 0 | 2 intronic |
| ANID_11152 | 1,3-beta-glucanosyltransferase | 1 conservative | 0 |
| ANID_12385 | hypothetical protein | 0 | 1 upstream, 2 intronic |
a
Non-synonymous SNP were classified as conservative if the BLOSUM80 score was 0 or higher for the substitution, or radical if the BLOSUM80 score was negative [74].
b
Other SNP include SNP in introns, untranslated regions (UTR) and within 100 bp upstream or downstream of the transcript. Synonymous SNP in coding regions are not included.
c
Protein domains for conserved hypothetical proteins were identified by a BLAST search of the Broad Institute database [38].
d
There are 3 SNP, but 2 affect the same codon.
e
No clear polymorphism, but ambiguity due to low sequence coverage for strain A91.
f
Premature stop codon.