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Detailed information for vg1207149149:

Variant ID: vg1207149149 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7149149
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATCTTTAGTGGCCTATTACCTTCACTATATATGTCATATGTGAACGCAGGACCCACCTAAGGGTATTTAGGTGTAGGTGAATGGTCTATAAGTGTCTG[G/A]
CATACCTACATCCTTATCCATATTCAAGGTGGTTCCGCTTTGAAATAGTGAATAAAATTCTCCAAAATCTTTCTTTAATGGTTTGGCTGATTCTTTTACC

Reverse complement sequence

GGTAAAAGAATCAGCCAAACCATTAAAGAAAGATTTTGGAGAATTTTATTCACTATTTCAAAGCGGAACCACCTTGAATATGGATAAGGATGTAGGTATG[C/T]
CAGACACTTATAGACCATTCACCTACACCTAAATACCCTTAGGTGGGTCCTGCGTTCACATATGACATATATAGTGAAGGTAATAGGCCACTAAAGATAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.60%	4.30%	13.10%	0.00%	NA
All Indica	2759	73.00%	7.00%	20.04%	0.00%	NA
All Japonica	1512	97.40%	0.30%	2.31%	0.00%	NA
Aus	269	89.60%	0.70%	9.67%	0.00%	NA
Indica I	595	84.20%	1.20%	14.62%	0.00%	NA
Indica II	465	58.10%	13.50%	28.39%	0.00%	NA
Indica III	913	75.90%	7.40%	16.65%	0.00%	NA
Indica Intermediate	786	69.80%	7.00%	23.16%	0.00%	NA
Temperate Japonica	767	95.40%	0.70%	3.91%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	1.10%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207149149	G -> A	LOC_Os12g12900-LOC_Os12g12910	intergenic_region ; MODIFIER	silent_mutation	Average:31.077; most accessible tissue: Callus, score: 47.819	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207149149	1.17E-07	NA	mr1024	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1207149149	2.89E-06	2.95E-07	mr1024	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251