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Detailed information for vg0206827776:

Variant ID: vg0206827776 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6827776
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

ACATATGATTAATTGAGTTTTAATTATTTTAAACATAAAAATAGATTTATTATATATTTTAAAGTAAATTTTGTATAGAAAATTATCACACGAAACGTAC[C/T]
GTTTAGCGGGTTGAAAACATGCTAATGAAAATCAAGATAAAATATATACGTTAATCAGGTCCAAACAGGGATCAGTGCTGAACTGATGAAGAAGTACATA

Reverse complement sequence

TATGTACTTCTTCATCAGTTCAGCACTGATCCCTGTTTGGACCTGATTAACGTATATATTTTATCTTGATTTTCATTAGCATGTTTTCAACCCGCTAAAC[G/A]
GTACGTTTCGTGTGATAATTTTCTATACAAAATTTACTTTAAAATATATAATAAATCTATTTTTATGTTTAAAATAATTAAAACTCAATTAATCATATGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.20%	28.40%	0.30%	22.13%	NA
All Indica	2759	46.00%	47.30%	0.22%	6.52%	NA
All Japonica	1512	63.90%	1.20%	0.40%	34.52%	NA
Aus	269	4.10%	0.00%	0.74%	95.17%	NA
Indica I	595	72.60%	27.10%	0.17%	0.17%	NA
Indica II	465	21.50%	65.40%	0.22%	12.90%	NA
Indica III	913	38.30%	57.10%	0.22%	4.38%	NA
Indica Intermediate	786	49.20%	40.50%	0.25%	10.05%	NA
Temperate Japonica	767	90.60%	0.80%	0.13%	8.47%	NA
Tropical Japonica	504	33.10%	1.00%	0.60%	65.28%	NA
Japonica Intermediate	241	43.20%	2.90%	0.83%	53.11%	NA
VI/Aromatic	96	29.20%	0.00%	0.00%	70.83%	NA
Intermediate	90	56.70%	21.10%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0206827776	C -> T	LOC_Os02g12930.1	downstream_gene_variant ; 594.0bp to feature; MODIFIER	silent_mutation	Average:34.759; most accessible tissue: Callus, score: 67.234	N	N	N	N
vg0206827776	C -> T	LOC_Os02g12939.1	downstream_gene_variant ; 3247.0bp to feature; MODIFIER	silent_mutation	Average:34.759; most accessible tissue: Callus, score: 67.234	N	N	N	N
vg0206827776	C -> T	LOC_Os02g12930-LOC_Os02g12939	intergenic_region ; MODIFIER	silent_mutation	Average:34.759; most accessible tissue: Callus, score: 67.234	N	N	N	N
vg0206827776	C -> DEL	N	N	silent_mutation	Average:34.759; most accessible tissue: Callus, score: 67.234	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206827776	NA	4.23E-13	mr1608	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
vg0206827776	NA	8.59E-08	mr1608	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
vg0206827776	NA	4.30E-10	mr1720	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