Table 1.

Illumina read data used and coverage of the concatenated RefBeet1.2 reference sequence

	Depth of coverage a	Read length b	Insert size c	Reference covered d
Breeding panel 1 red	24.72 x	150	500	66.5
Breeding panel 1 green	23.60 x	150	500	62.0
Breeding panel 2 red	25.60 x	150	500	64.4
Breeding panel 2 green	25.08 x	150	500	63.0
Breeding panel 3 red	19.41 x	150	500	47.2
Breeding panel 3 green	23.45 x	150	500	62.9
Breeding panel 2 red total	73.27 x	100/150	450/500	90.0
Breeding panel 2 green total	69.69 x	100/150	450/500	89.3
Superpool red	76.14 x	100/150	450/500	91.7
Superpool green	78.41 x	100/150	450/500	91.9

^a Mean number of uniquely mapped reads covering each base of the reference sequence

^b Length of the sequenced reads in base pairs; if more than one number is shown, two datasets with differing read length were merged; all generated as paired ends (PE)

^c Targeted length of the PE sequenced fragments in base pairs; if more than one number is shown, two datasets with differing read length were merged

^d Percentage of the reference sequence with more than 15 fold read coverage