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Detailed information for vg0318673691:

Variant ID: vg0318673691 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18673691
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.06, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCAATCCAAAACAAATATATTATGAAAAAATATTCAATTATAAATTTAATAAAACTAATTTGTCTATAAACTTGATCAAATTTGATCCGGAACTAAA[G/A]
ATACCATCTTTAGTCTAGAATTTGGGGGTCCCGGTTTGCAACCCGGGATATAGGGGGTTGTAAACTGGGACAATTGAGGTTTCTCCACCAGTGAGAACTA

Reverse complement sequence

TAGTTCTCACTGGTGGAGAAACCTCAATTGTCCCAGTTTACAACCCCCTATATCCCGGGTTGCAAACCGGGACCCCCAAATTCTAGACTAAAGATGGTAT[C/T]
TTTAGTTCCGGATCAAATTTGATCAAGTTTATAGACAAATTAGTTTTATTAAATTTATAATTGAATATTTTTTCATAATATATTTGTTTTGGATTGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.30%	46.80%	0.80%	0.00%	NA
All Indica	2759	77.80%	21.70%	0.47%	0.00%	NA
All Japonica	1512	1.50%	97.00%	1.46%	0.00%	NA
Aus	269	90.00%	10.00%	0.00%	0.00%	NA
Indica I	595	92.80%	7.10%	0.17%	0.00%	NA
Indica II	465	73.10%	26.50%	0.43%	0.00%	NA
Indica III	913	68.70%	31.00%	0.33%	0.00%	NA
Indica Intermediate	786	79.80%	19.30%	0.89%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	3.80%	96.00%	0.20%	0.00%	NA
Japonica Intermediate	241	0.80%	90.50%	8.71%	0.00%	NA
VI/Aromatic	96	25.00%	71.90%	3.12%	0.00%	NA
Intermediate	90	43.30%	56.70%	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
vg0318673691	G -> A	LOC_Os03g32620.1	downstream_gene_variant ; 4133.0bp to feature; MODIFIER	silent_mutation	Average:45.139; most accessible tissue: Callus, score: 73.16	N	N	N	N
vg0318673691	G -> A	LOC_Os03g32610-LOC_Os03g32620	intergenic_region ; MODIFIER	silent_mutation	Average:45.139; most accessible tissue: Callus, score: 73.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318673691	1.01E-06	NA	mr1439	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
vg0318673691	4.02E-08	1.83E-07	mr1439	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
vg0318673691	NA	2.06E-06	mr1718	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
vg0318673691	NA	6.31E-09	mr1835_2	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
vg0318673691	NA	5.50E-11	mr1893_2	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