Table 3.

Nucleotide position of the polymorphism, sequence of the single base extension primer including polymeric T-stretch (5′ → 3′), orientation of the primer, primer length (bp), Tm of primer (°C), GC content of primer (%), final concentration (nM) of each minisequencing primer, and the expected base substitution observed at the polymorphic site*

Nucleotide position	Primer sequence	Orientation	Primer length (bp)	Tm (°C)	GC content (%)	Final (nM)	Base substitution
	(5′ → 3′)
8272-8280 del	CCCTATAGCACCCCCTCTA	F	19	54.9	57.8	84	C>G
13263	(3-poly-T tail)-TAGCCTTCTCCACTTCAAGTCA	F	25	56.3	40.0	83	A>G
1719	(9-poly-T tail)-CACTCCACCTTACTACCAGACAAC	F	33	59.2	36.3	292	G>A
5178	(13-poly-T tail)-CTACTATCTCGCACCTGAAACAAG	F	37	58.5	29.7	167	C>A
663	(19-poly-T tail)-CCATAAACAAATAGGTTTGGTCCT	F	43	58.8	20.9	84	A>G
10398	(21-poly-T tail)-GAGTGACTACAAAAAGGATTAGACTGA	F	48	59.7	20.8	292	A>G
10400	(24-poly-T tail)-TTCGTTTTGTTTAAACTATATACCAATTC	R	53	58.4	13.2	292	C>T
3594	(29-poly-T tail)-TAGGAGGCCTAGGTTGAGGTT	R	58	62.2	20.6	167	C>T
7028	(33-poly-T tail)-CCTATTGATAGGACATAGTGGAAGTG	R	63	62.6	20.6	84	C>T
12406	(50-poly-T tail)-CCCATCCTTACCACCCTC	F	68	63.5	16.1	167	G>A
4833	(54-poly-T tail)-CCAGAGGTTACCCAAGGC	F	73	64.7	16.4	292	A>G
7600	(51-poly-T tail)-TATCTTAATGGCACATGCAGC	F	78	64.1	12.8	166	G>A

*For the single base extension primers designed in the reverse orientation the recorded base substitution remains in the forward orientation to facilitate interpretation