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Detailed information for vg0304640187:

Variant ID: vg0304640187 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 4640187
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, A: 0.01, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTGATATATTGTTTAAAGTACATGTAGTTTTGTGATAAACAAAGACATTAAATCTGTAGTTTTGTGAAACTAGTTCTAAAATCTATAGTTTTGCGATA[G/T]
ATTGTGCAAAGTATATGTAGTTTTATGAAATTTACTCATAAAACAAACTTAAGACTAAATGTGATATACTAAAACAAATCTAGAATTAGATGTGAAATAT

Reverse complement sequence

ATATTTCACATCTAATTCTAGATTTGTTTTAGTATATCACATTTAGTCTTAAGTTTGTTTTATGAGTAAATTTCATAAAACTACATATACTTTGCACAAT[C/A]
TATCGCAAAACTATAGATTTTAGAACTAGTTTCACAAAACTACAGATTTAATGTCTTTGTTTATCACAAAACTACATGTACTTTAAACAATATATCACAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.50%	49.40%	0.08%	0.02%	NA
All Indica	2759	22.90%	76.90%	0.14%	0.04%	NA
All Japonica	1512	97.60%	2.40%	0.00%	0.00%	NA
Aus	269	51.30%	48.70%	0.00%	0.00%	NA
Indica I	595	11.90%	88.10%	0.00%	0.00%	NA
Indica II	465	25.40%	74.40%	0.22%	0.00%	NA
Indica III	913	26.90%	72.90%	0.11%	0.00%	NA
Indica Intermediate	786	25.20%	74.40%	0.25%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	93.10%	6.90%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	60.00%	40.00%	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
vg0304640187	G -> T	LOC_Os03g08940.1	downstream_gene_variant ; 3872.0bp to feature; MODIFIER	silent_mutation	Average:32.249; most accessible tissue: Callus, score: 62.544	N	N	N	N
vg0304640187	G -> T	LOC_Os03g08940-LOC_Os03g08950	intergenic_region ; MODIFIER	silent_mutation	Average:32.249; most accessible tissue: Callus, score: 62.544	N	N	N	N
vg0304640187	G -> DEL	N	N	silent_mutation	Average:32.249; most accessible tissue: Callus, score: 62.544	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0304640187	3.81E-07	NA	mr1739	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
vg0304640187	2.82E-07	NA	mr1739	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