Table 8.

Pseudoallele frequency (PAF).

OR name	SNP type	SNP position	GSD	BM	ESS	Grey	LR	Pek	6 breeds
CfOR0004	indel	351	0.062	0.562	0.188	0.438	0.125	0.062	0.24
	NS	823	0.688	0.312	0.375	0.438	0.562	0.562	0.49
	indel	468	0.188	0.062	0	0	0	0	0.042
CfOR0043	NS	737	0.812	0.875	0.812	1	0.938	0.438	0.812
CfOR0135	indel	27	0	0	0.062	0	0	0	0.01
CfOR0180	indel	89	0	0.062	0.062	0	0	0	0.021
CfOR0401	NS	49	0	0	0.062	0	0	0	0.01
CfOR0438	indel	20	0.625	1	0.875	0.812	0.562	0.938	0.802
CfOR04C05	indel	70	0	0	0	0	0	0.125	0.021
CfOR0519	NS	306	1	1	1	0.938	1	1	0.99
	indel	289	0.062	0	0	0	0.188	0	0.042
	indel	536	0	0	0	0.188	0	0.062	0.042
CfOR0565	NS	790	0	0.062	0.062	0	0	0	0.021
CfOR0821	NS	84	0	0	0	0	0	0.125	0.021
CfOR08G02	NS	360	0.812	0.375	0.125	0.188	0.438	0.062	0.333
CfOR12F06	NS	1	0.875	0.5	0.375	0.25	0.75	0.375	0.521
CfOR14A11	indel	362	0.125	0.75	0.375	0.75	1	0.125	0.521
	indel	204	0	0.125	0	0	0	0.25	0.062
CfOR16C11	indel	633	0.125	0.188	0.438	0.25	0.188	0	0.198
CfOR3109	indel	89	1	1	0.625	0.428	0.75	1	0.798
	indel	306	0	0	0	0.143	0	0	0.024
CfOR5912	NS	658	0.25	0.188	0	0.188	0.312	0.062	0.167

PAF was calculated independently for each breed and for the whole population. Pseudoallele distribution varies considerably between breeds, with some pseudoalleles present in all breeds and some in only one or a few breeds: 9 are common to all breeds, 5 are found in only one breed and 8 are shared by two to five breeds, giving 10, 12, 13, 10, 10 and 11 OR pseudogenes for GSD, BM, ESS, Grey, LR and Pek, respectively. NS: nonsense, indel: insertion/deletion.