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Detailed information for vg0225316083:

Variant ID: vg0225316083 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25316083
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTGATGCCAATATTATGTACGTATTTGTGATGCTCTGGATTTGGATTGTGTTTAAATGATGTTTATGCCCATTTCTAAATATGGATTGTTTTGAATTTG[G/A]
CCGGGTGGGGAATTTTGAATTTGGGGTAGGGAATTTTTGGCGGGGTGGGTTGATTTTCATTGGCGGTTCTCTTTAAACAACCGCCAGAGAAAATGGGTTT

Reverse complement sequence

AAACCCATTTTCTCTGGCGGTTGTTTAAAGAGAACCGCCAATGAAAATCAACCCACCCCGCCAAAAATTCCCTACCCCAAATTCAAAATTCCCCACCCGG[C/T]
CAAATTCAAAACAATCCATATTTAGAAATGGGCATAAACATCATTTAAACACAATCCAAATCCAGAGCATCACAAATACGTACATAATATTGGCATCAAT

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	50.10%	13.90%	0.42%	35.63%	NA
All Indica	2759	42.90%	3.40%	0.43%	53.28%	NA
All Japonica	1512	59.70%	36.30%	0.26%	3.70%	NA
Aus	269	63.20%	0.00%	0.37%	36.43%	NA
Indica I	595	26.90%	0.50%	0.50%	72.10%	NA
Indica II	465	49.70%	1.50%	0.22%	48.60%	NA
Indica III	913	46.90%	6.20%	0.11%	46.77%	NA
Indica Intermediate	786	46.40%	3.30%	0.89%	49.36%	NA
Temperate Japonica	767	64.10%	34.90%	0.52%	0.39%	NA
Tropical Japonica	504	53.00%	37.10%	0.00%	9.92%	NA
Japonica Intermediate	241	59.80%	39.00%	0.00%	1.24%	NA
VI/Aromatic	96	64.60%	0.00%	2.08%	33.33%	NA
Intermediate	90	52.20%	15.60%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0225316083	G -> A	LOC_Os02g42110.1	upstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:30.347; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0225316083	G -> A	LOC_Os02g42100-LOC_Os02g42110	intergenic_region ; MODIFIER	silent_mutation	Average:30.347; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N
vg0225316083	G -> DEL	N	N	silent_mutation	Average:30.347; most accessible tissue: Zhenshan97 panicle, score: 71.253	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225316083	3.92E-06	NA	mr1122	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