Table 4

Characteristics and in silico prediction of non-neutral non-synonymous changes

Sites (bp) NC_012011

SNP

Amino acid change

Amino acid substitutions characteristics

SIFT prediction (score)

3763971

SNP 772 (G/A)

T131A

polar neutral/non-polar neutral

tolerated

(1.00)

3762959

SNP 1784 (T/C)

S272P

polar neutral/non-polar neutral

affect protein function (0.00)

3762921

SNP 1822 (G/T)

K284N

polar basic/polar neutral

affect protein function (0.00)

3762761

SNP 1982 (C/T)

R306C

polar basic/slightly polar neutral

affect protein function (0.00)

3760773

SNP 3970 (G/A)

T514A

polar neutral/non-polar neutral

tolerated

(0.85)

3760635

SNP 4108 (G/A)

V560I

non-polar neutral

tolerated

(0.11)

3760608

SNP 4135 (A/G)

I569V

non-polar neutral

tolerated

(0.40)

3760485

SNP 4258 (G/A)

R584K

polar basic

tolerated

(0.31)

3760434

SNP 4309 (C/T)

S601F

polar neutral/non-polar neutral

affect protein function (0.01)

3759957

SNP 4786 (C/T)

L716S

non-polar neutral/polar neutral

low confidence prediction

SNPs are named and scored according to their position on VvDXS ORF of V. vinifera PN40024; sites are referenced to the nucleotide positions relative to locus NC_012011. Low confidence prediction means there were not enough comparisons at that site.

Emanuelli et al. BMC Plant Biology 2010 10:241   doi:10.1186/1471-2229-10-241