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

Table 1 Identification of unique and candidate SNPs in the parental and mutant genomes

	*bak1*-5	*bak1-5 mob1*	*bak1-5 mob2*
Total SNPs compared to Col-0 TAIR10	2639	4188	3581
Unique SNPs compared to the parent	2639	1633	1006
Unique SNPs, AF >75%	785	88	143
Unique SNPs, AF >75%, annotated coding	240	16	41
Unique SNPs, AF >75%, annotated coding, non-synon	168	9^a	31^b

To identify SNPs unique to each genome, the parental and mutant genomes were compared and filtered. Unique SNPs in bak1-5 refer to those that are not found in the Col-0 TAIR10 genome. For the bak1-5 mob1 and bak1-5 mob2 datasets, SNPs shared between any of the three genomes (bak1-5, bak1-5 mob1 and bak1-5 mob2; Figure 3B) were removed, resulting in SNPs uniquely found in each of those genomes. Filtering for SNPs with an allele frequency higher than 75% that cause non-synonymous (‘non-synon’) changes in annotated coding regions resulted in a list of candidate causative mutations.
^aCandidate causative SNPs for bak1-5 mob1 are listed in Table 2.
^bCandidate causative SNPs for bak1-5 mob2 are listed in Table 3.