Table 2.
Candidate causative SNPs in bak1 - 5 mob1
| Chr | Position | Ref/Alt | AF (%) | AGI | Gene ID | AA change | Sanger F 3 |
|---|---|---|---|---|---|---|---|
| 1 | 11892068 | C/T | 100 | At1g32830 | Transposable element | n.a. | Absent |
| 1 | 11892070 | G/T | 100 | At1g32830 | Transposable element | n.a. | Homa |
| 1 | 11892252 | T/G | 100 | At1g32830 | Transposable element | n.a. | Homa |
| 1 | 16516501 | T/C | 83.3 | At1g43745 | Transposable element | n.a. | Absent |
| 1 | 16525522 | T/C | 77.8 | At1g43755 | Transposable element | n.a. | Homa |
| 1 | 24243231 | G/A | 80.9 | At1g65270 | Unknown protein | G > S | Hom |
| 5 | 26457834 | G/A | 85.0 | At5g66210 | CPK28 | A > V | Homb |
| 5 | 26458077 | G/A | 78.5 | At5g66210 | CPK28 | S > L | Homb |
| 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].