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Detailed information for vg0302286904:

Variant ID: vg0302286904 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 2286904
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCAATCCACTCGACGCAGGTCATTAGTGAAGGCAGCTACTCCATCCACGTCGTCGTCGTAGCGATTTGGTGAATGGCGGTGATCTCGTGCTGCACGGC[G/A]
CTGGTTGATCGTGTCGTGAAGGTCGACGGGACGCCGGTGAGGTGGAGAGCGAGGCCGTTTGACTCGGCGCTCCCTGTGACGTTCAGGAGGCGAGTGAACA

Reverse complement sequence

TGTTCACTCGCCTCCTGAACGTCACAGGGAGCGCCGAGTCAAACGGCCTCGCTCTCCACCTCACCGGCGTCCCGTCGACCTTCACGACACGATCAACCAG[C/T]
GCCGTGCAGCACGAGATCACCGCCATTCACCAAATCGCTACGACGACGACGTGGATGGAGTAGCTGCCTTCACTAATGACCTGCGTCGAGTGGATTGGCC

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	64.20%	35.60%	0.19%	0.00%	NA
All Indica	2759	48.10%	51.80%	0.14%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	33.10%	65.40%	1.49%	0.00%	NA
Indica I	595	63.50%	36.30%	0.17%	0.00%	NA
Indica II	465	22.20%	77.60%	0.22%	0.00%	NA
Indica III	913	53.60%	46.20%	0.22%	0.00%	NA
Indica Intermediate	786	45.30%	54.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	38.50%	1.04%	0.00%	NA
Intermediate	90	64.40%	35.60%	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
vg0302286904	G -> A	LOC_Os03g04810.1	missense_variant ; p.Arg379Cys; MODERATE	nonsynonymous_codon ; R379C	Average:15.266; most accessible tissue: Zhenshan97 flower, score: 19.853	benign	0.467	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0302286904	NA	1.42E-06	mr1593	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
vg0302286904	4.91E-06	4.91E-06	mr1955	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