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

Table 3 Comparison of SNPs in the IL and DL datasets at different read depth levels

Read depth	IH		HE		S
Nr. of common positions*
6	34280		43743		10469
8	27514		34163		8025
10	22220		26900		6277
SNP variants in the DL assembly**
		%		%		%
6	28756	83.89	28393	64.91	5992	57.24
8	23537	85.55	22759	66.19	4767	59.4
10	19626	88.33	18793	69.86	3915	62.37

IH: Inter-homeolog SNPs, HE: Hemi-SNPs, S: Simple SNPs.
*Number of reference sequence positions where short read coverages were at or above the applied read depth threshold (given in the first column) for both read types in the IL assembly, as well as in the DL assembly.
**Number and percentage (in italics) of DL variants with ambiguity consensus code in matching positions. Note that no base quality filtering was applied for this comparison when searching for matching DL variants.

ISSN: 1471-2164