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Detailed information for vg0225261737:

Variant ID: vg0225261737 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25261737
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.29, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGAATAGGGAAGTATACATTGCTAGATGGATATGTGTCATAACTTAACCAAGGGCGGAGGTAAAGTATAGGAGGGGGAGGGGGGTGCTGAGGAACCCA[G/A]
TTAAGAAATTTTTTTAGCTATATATCACCTATTTTTCACTATGTGTTCACCCCCCCTCAGTACAAAAGACTTAGGAACCCACATCAACTTAAATTTGATC

Reverse complement sequence

GATCAAATTTAAGTTGATGTGGGTTCCTAAGTCTTTTGTACTGAGGGGGGGTGAACACATAGTGAAAAATAGGTGATATATAGCTAAAAAAATTTCTTAA[C/T]
TGGGTTCCTCAGCACCCCCCTCCCCCTCCTATACTTTACCTCCGCCCTTGGTTAAGTTATGACACATATCCATCTAGCAATGTATACTTCCCTATTCCCA

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	58.80%	40.70%	0.49%	0.00%	NA
All Indica	2759	41.80%	57.60%	0.62%	0.00%	NA
All Japonica	1512	92.40%	7.40%	0.20%	0.00%	NA
Aus	269	43.90%	55.80%	0.37%	0.00%	NA
Indica I	595	23.20%	75.50%	1.34%	0.00%	NA
Indica II	465	49.70%	50.10%	0.22%	0.00%	NA
Indica III	913	46.90%	53.10%	0.00%	0.00%	NA
Indica Intermediate	786	45.30%	53.70%	1.02%	0.00%	NA
Temperate Japonica	767	98.60%	1.30%	0.13%	0.00%	NA
Tropical Japonica	504	86.10%	13.70%	0.20%	0.00%	NA
Japonica Intermediate	241	85.90%	13.70%	0.41%	0.00%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	56.70%	41.10%	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
vg0225261737	G -> A	LOC_Os02g42030.1	upstream_gene_variant ; 423.0bp to feature; MODIFIER	silent_mutation	Average:42.948; most accessible tissue: Callus, score: 63.692	N	N	N	N
vg0225261737	G -> A	LOC_Os02g42020-LOC_Os02g42030	intergenic_region ; MODIFIER	silent_mutation	Average:42.948; most accessible tissue: Callus, score: 63.692	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225261737	4.08E-06	4.08E-06	mr1621	Jap_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
vg0225261737	NA	1.66E-06	mr1042_2	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
vg0225261737	NA	7.27E-06	mr1291_2	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
vg0225261737	NA	4.97E-10	mr1457_2	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
vg0225261737	NA	4.10E-06	mr1892_2	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