Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions

BMC Genomics

Table 2 CAPS and Sanger validation of variants in multiple single plants of an accession

Gene	Pos^a	Ref^b	Alt^c	Method	RE used	Acc^d	GATK^e	SNVer^e	CRISP^e	VAFobs^f	No. plants^g
MATE1	170	A	G	CAPS	NotI	D2	0.880	0.587	0.819	0.79	26[11]
MATE1	170	A	G	CAPS	NotI	E12	0.875	0.592	0.783	0.70	27[8]
MATE1	210	A	G	CAPS	TaqI	H5	0.172	0.079	0.276	0.38	25[15]
MATE1	364	G	C	CAPS	MboI	H5	0.307	0.137	0.393	0.24	25[8]
PBF	310	C	T	CAPS	MnlI	D2	0.292	0.206	0.165	0.44	25[14]
PBF	310	C	T	CAPS	MnlI	E12	0.120	0.059	0.059	0.10	25[5]
PBF	517	G	A	CAPS	MboI	D2	0.286	0.262	0.180	0.44	27[12]
PBF	517	G	A	CAPS	MboI	E12	0.016	0.104	0.065	0.09	27[5]
PBF	532	C	T	CAPS	FokI	D2	0.104	0.096	0.138	0.00	26[0]
PBF	532	C	T	CAPS	FokI	E12	0.536	0.405	0.472	0.43	25[14]
PBF	666	C	T	Sanger	na^h	F8	0.401	0.371	0.359	0.58	25[11]
PBF	810	C	T	Sanger	na	F10	0.042	0.022	0.068	0.00	6[0]
PBF	810	C	T	Sanger	na	F11	0.214	0.074	0.216	0.16	16[5]
PBF	846	G	C	Sanger	na	F8	0.094	0.053	0.104	0.10	25[5]
PBF	847	G	A	Sanger	na	F8	0.094	0.064	0.100	0.08	25[4]
Sinb	211	A	G	CAPS	FokI	H5	0.026	0.183	0.111	0.00	25[0]

ISSN: 1471-2164