Table 2 Genetic models and filtration chains
Inheritance model | 1 | 2 | 3 | 4 | 5 | 6 |
|---|---|---|---|---|---|---|
Auto dominant | Auto dominant | Auto recessive | Auto recessive | Auto dominant | Auto recessive | |
Paternal affected | Maternal affected | Paternal affected | Maternal affected | Myco susceptible | Myco susceptible | |
Reference genome | 38 | 38 | 38 | 38 | 38 | 38 |
Sequence ontology (variant locations) | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD |
Allele annotation source | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 |
Minor allele frequency | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing |
Affected members | 4, 5, 6, 12 | 5, 6, 8, 9, 11, 14 | 4, 5, 6, 12 | 5, 6, 8, 9, 11, 14 | 4, 5, 6, 12 | 4, 5, 6, 12 |
Unaffected member | 3 | 10 | 3 | 10 | 10 | 10 |
Sharing filter (number of affected members) | all N (=4) | all N (=6) | all N (=4) | all N (=6) | all N (=4) | all N (=4) |
Zygosity filter | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes | Homozygous minor allele | Homozygous minor allele | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes |
Sequence read depth filter | 10 or greater | 10 or greater | 10 or greater | 10 or greater | 10 or greater | 10 or greater |
Polyphen status (probably or possibly damaging mutation) or not called by Polyphen | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called |
Inheritance model | 7 | 8 | 9 | 10 | 11 | 12 |
|---|---|---|---|---|---|---|
Auto dominant | Auto dominant | Auto recessive | Auto Recessive | Auto dominant | Auto recessive | |
Paternal affected | Maternal affected | Paternal affected | Maternal affected | Myco susceptible | Myco susceptible | |
Reference genome | 38 | 38 | 38 | 38 | 38 | 38 |
Sequence ontology (variant locations) | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD | Coding + SA/SD |
Allele annotation source | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 | Ensembl Genes90 |
Minor allele frequency from 1 K genomes | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing | Less than 0.05 or missing |
Affected members | 4, 5, 6, 12 | 5, 6, 8, 9, 11, 14 | 4, 5, 6, 12 | 5, 6, 8, 9, 11, 14 | 4, 5, 6, 12 | 4, 5, 6, 12 |
Unaffected member | 3 | 10 | 3 | 10 | 10 | 10 |
Sharing filter (number of affected members) | N − 1(=3) | N − 1(=5) | N − 1(=3) | N − 1(=5) | N − 1(=3) | N − 1(=3) |
Zygosity filter | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes | Homozygous minor allele + heterozygotes |
Sequence read depth filter | 10 or greater | 10 or greater | 10 or greater | 10 or greater | 10 or greater | 10 or greater |
Polyphen status (probably or Possibly damaging mutation) or not called by Polyphen | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called | Possibly or probably or not called |