Chado designation	SO ID	SO name	Comment
amino_acid_mutation	SO:0001606	amino_acid_substitution
nucleotide_mutation	SO:0001576	transcript_variant
deletion	SO:0001893	transcript_ablation
partial_amino_acid_deletion	SO:0001604	amino_acid_deletion
partial_nucleotide_deletion	SO:0001906	feature_truncation
nonsense_mutation	SO:0001587	stop_gained
wild_type	SO:0000817	wild_type	under 'attribute' in SO, not 'variant' branch
disruption	?	is an insertion of a marker (maybe SO:0001838, although marker may be exogenous (e.g. KanMX) or a pombe sequence (e.g. ura4+)), and may or may not also include deletion of some wild type nucleotides
unrecorded	N/A	only used to store a few legacy phenotype annotations
unknown	SO:0001537	structural_variant
other	SO:0001537	structural_variant