Mapping mutations in plant genomes with the user-friendly web application CandiSNP

Table 2 Candidate causative SNPs in bak1 - 5 mob1

Chr	Position	Ref/Alt	AF (%)	AGI	Gene ID	AA change	Sanger F₃
1	11892068	C/T	100	At1g32830	Transposable element	n.a.	Absent
1	11892070	G/T	100	At1g32830	Transposable element	n.a.	Hom^a
1	11892252	T/G	100	At1g32830	Transposable element	n.a.	Hom^a
1	16516501	T/C	83.3	At1g43745	Transposable element	n.a.	Absent
1	16525522	T/C	77.8	At1g43755	Transposable element	n.a.	Hom^a
1	24243231	G/A	80.9	At1g65270	Unknown protein	G > S	Hom
5	26457834	G/A	85.0	At5g66210	CPK28	A > V	Hom^b
5	26458077	G/A	78.5	At5g66210	CPK28	S > L	Hom^b
5	26474069	G/A	76.5	At5g66270	Zn-finger family protein	P > L	Hom

Unique SNPs in annotated coding regions with allele frequencies (AF) over 75% identified by CandiSNP for bak1-5 mob1, listing the Chromosome number (Chr), position, reference base (Ref), sequenced alternate base (Alt), locus number (AGI), gene identification (Gene ID), amino acid change (AA change; ‘n.a.’ is not applicable). All SNPs were confirmed in at least three independent back-crossed lines (F₃ generation) by Sanger sequencing compared to bak1-5. SNPs that were homozygous (Hom) or not present (Absent) are listed.
^aThese SNPs were also identified in bak1-5 by Sanger sequencing (however, not by Illumina sequencing) and are therefore not unique to bak1-5 mob1.
^bThese SNPs are the causative mutations for bak1-5 mob1[13].

ISSN: 1746-4811