Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize

BMC Plant Biology

Table 3 Polymorphic sites causing amino acid changes in the protein of GRMZM2G039934

Gene ID	Amino acid substitution (Huangzaosi/LV28)^a	PROVEAN score^b	Prediction (cutoff = −2.5)^c
GRMZM2G039934	R42C	−0.43	Neutral
	T55I	−3.72	Deleterious
	Q371R	−0.82	Neutral
	I375L	0.16	Neutral
	M380V	0.26	Neutral
	N386K	−0.09	Neutral
	K387I	−1.16	Neutral
	D388N	−0.65	Neutral

Notes: ^aAmino acid substitution format is X#Y, where X is the original amino acid, # is the position of the substitution, and Y is the new amino acid. ^bA delta alignment score is computed for each supporting sequence. The scores are then averaged within and across clusters to generate the final PROVEAN score. If the PROVEAN score is equal to or below a predefined threshold (e.g., −2.5), the protein variant is predicted to have a “deleterious” effect. If the PROVEAN score is above the threshold, the variant is predicted to have a “neutral” effect; ^cfor maximum separation of the deleterious and neutral protein variants, the default score threshold is currently set at −2.5 for binary classification

ISSN: 1471-2229