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Detailed information for vg0318113258:

Variant ID: vg0318113258 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18113258
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCATTGTTTTCGCGTAGGGGGCGATTTAGGTTTTGTTCGTTGCCTGGATTTTTGGGCTGTTGTAGGATTGGATGGGAGTTTTTTAATTTGTTGGGTGT[T/G]
TTCACGTCTGTCCTGTTGCGGCTAAAGTTGGATTTGTCTAGGTTTTTTTTCCACTGTAGGATCGATTTTGAATTTTTGATCCGTGCAATCGCACGGCTTG

Reverse complement sequence

CAAGCCGTGCGATTGCACGGATCAAAAATTCAAAATCGATCCTACAGTGGAAAAAAAACCTAGACAAATCCAACTTTAGCCGCAACAGGACAGACGTGAA[A/C]
ACACCCAACAAATTAAAAAACTCCCATCCAATCCTACAACAGCCCAAAAATCCAGGCAACGAACAAAACCTAAATCGCCCCCTACGCGAAAACAATGACC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.40%	1.80%	1.82%	0.00%	NA
All Indica	2759	94.00%	3.00%	3.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	76.30%	12.10%	11.60%	0.00%	NA
Indica II	465	99.40%	0.00%	0.65%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	97.30%	1.30%	1.40%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0318113258	T -> G	LOC_Os03g31706.2	upstream_gene_variant ; 600.0bp to feature; MODIFIER	silent_mutation	Average:58.708; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0318113258	T -> G	LOC_Os03g31706-LOC_Os03g31730	intergenic_region ; MODIFIER	silent_mutation	Average:58.708; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318113258	NA	2.07E-06	mr1662	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0318113258	1.38E-06	1.96E-06	mr1887	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