Comprehensive analysis of geographic and breed-purpose influences on genetic diversity and inherited disease risk in the Doberman dog breed

Table 5 Attributes of variants in regions larger than 500 Kb observed as homozygous in 90% of Dobermans in any locale-purpose cohort. Variants are not filtered for FST

Chromosome	2	3	3	23	27	31	31
Region (Mb range)	60–64	1–2	57–59	46–48	13.3–13.8	1–1.2	4–6
Regional Variants ^a (1,527 dogs)	167,349	53,239	70,777	51,350	23,993	57,976	68,953
Polymorphic Variants (1,527 dogs)	166,008	52,629	70,303	51,035	23,871	57,492	68,445
Array ^b Markers (1,527 dogs)	4,375	812	4,765	3,615	315	4,230	934
Observed Functional Variants ^c (1,527 dogs)	713	429	854	312	57	298	64
Polymorphic Variants (8 Dobermans)	4,375	812	4,765	3,615	315	4,230	934
Polymorphic Array ^b markers (8 Dobermans)	32	5	76	48	1	3	-
Functional Polymorphic Variants ^c (8 Dobermans)	65	10	84	43	2	9	1
Monomorphic, Alternate allele ^d, Functional ^c (8 Dobermans)	9	1	9	1	1	-	5
Locale-purpose clusters that have regions of concern	0, 2A, 3A	All	All	0, 2A, 3A	2A	All	All

^aMarkers are polymorphic in any one of 1,257 dogs
^bVariants represented in array genotype data and variant call files from dogs with whole genome sequence
^cVariants identified as putatively functional in the Jagannathan et al. variant call file (Jagannathan et al. 2019)
^dAlternate allele is relative to the wider population consensus main allele and not the reference

ISSN: 2662-9380