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Detailed information for vg0300976326:

Variant ID: vg0300976326 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 976326
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGCATAAAGCTGCCAAATCTGACAAGGGCTATGGTTTCTATGTTGACAATACAATTGGAAGGTACCATATCCCTTATGTCTGCACACTATAAGTTTC[G/A]
TGAAACATGGTATATCAATCAAGTTTCCTTGCAATATCTATCTTGAGCTTTTCTAATCATCCTTTTTACTGTAGCACTCCGCAAATTAACACTTGGACTG

Reverse complement sequence

CAGTCCAAGTGTTAATTTGCGGAGTGCTACAGTAAAAAGGATGATTAGAAAAGCTCAAGATAGATATTGCAAGGAAACTTGATTGATATACCATGTTTCA[C/T]
GAAACTTATAGTGTGCAGACATAAGGGATATGGTACCTTCCAATTGTATTGTCAACATAGAAACCATAGCCCTTGTCAGATTTGGCAGCTTTATGCATTT

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	92.80%	7.20%	0.06%	0.00%	NA
All Indica	2759	88.20%	11.70%	0.11%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	66.00%	33.30%	0.65%	0.00%	NA
Indica III	913	97.50%	2.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.90%	14.10%	0.00%	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	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg0300976326	G -> A	LOC_Os03g02650.1	upstream_gene_variant ; 2490.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0300976326	G -> A	LOC_Os03g02640.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0300976326	3.38E-06	NA	mr1004_2	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