A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover

Table 1 SNP categories found in the IL dataset

SNP types	Contigs		Singlets
Sub-categories	Nr.	%	Nr.	%
Hemi-SNPs	65147	43.26	8424	38.41
Inter-homeolog SNPs	46780	31.06	6883	31.38
Congruent consensus	46765		6881
Non-congruent consensus	15		2
Simple SNPs	18534	12.31	1419	6.47
CONS1 is the same as REF	18007		1314
CONS2 is the same as REF	525		105
Others	2		0
Irregular SNPs	20136	13.37	5208	23.74
Low coverage (0 to 5) in the opposing read type	13583		4461
Departure from REF	6539		747
More than 2 alleles in one genotype	14		0
Total	150597		21934

ISSN: 1471-2164