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Detailed information for vg0808817077:

Variant ID: vg0808817077 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8817077
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, A: 0.06, T: 0.02, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

CTACGAACCGATCACACCGTTGTATTCGTTGCAATTAAATCTTTAGAACAAGATATCATATGATTATATTATGTCAAAAGAAAAAACATGTGTTTCAAAC[C/A,T]
GTTAAAACTAAACGTTTCATACATGATAGTGATATATTTCAATGCGTGTGTTTCGATATGTTTCACAAAGTTCTTGAAACTACCTGTTACTAGTCTCTTT

Reverse complement sequence

AAAGAGACTAGTAACAGGTAGTTTCAAGAACTTTGTGAAACATATCGAAACACACGCATTGAAATATATCACTATCATGTATGAAACGTTTAGTTTTAAC[G/T,A]
GTTTGAAACACATGTTTTTTCTTTTGACATAATATAATCATATGATATCTTGTTCTAAAGATTTAATTGCAACGAATACAACGGTGTGATCGGTTCGTAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.00%	20.20%	6.50%	18.30%	T: 0.04%
All Indica	2759	38.00%	29.50%	10.58%	21.89%	T: 0.07%
All Japonica	1512	86.40%	2.40%	0.20%	11.04%	NA
Aus	269	71.00%	0.00%	1.49%	27.51%	NA
Indica I	595	34.50%	32.90%	12.77%	19.83%	NA
Indica II	465	23.90%	48.60%	14.19%	13.33%	NA
Indica III	913	55.20%	10.60%	6.24%	27.93%	NA
Indica Intermediate	786	29.00%	37.40%	11.83%	21.50%	T: 0.25%
Temperate Japonica	767	95.30%	3.10%	0.00%	1.56%	NA
Tropical Japonica	504	77.00%	0.60%	0.60%	21.83%	NA
Japonica Intermediate	241	77.60%	3.70%	0.00%	18.67%	NA
VI/Aromatic	96	13.50%	81.20%	0.00%	5.21%	NA
Intermediate	90	43.30%	31.10%	8.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808817077	C -> T	LOC_Os08g14660.1	upstream_gene_variant ; 378.0bp to feature; MODIFIER	silent_mutation	Average:9.997; most accessible tissue: Callus, score: 45.75	N	N	N	N
vg0808817077	C -> T	LOC_Os08g14660-LOC_Os08g14670	intergenic_region ; MODIFIER	silent_mutation	Average:9.997; most accessible tissue: Callus, score: 45.75	N	N	N	N
vg0808817077	C -> A	LOC_Os08g14660.1	upstream_gene_variant ; 378.0bp to feature; MODIFIER	silent_mutation	Average:9.997; most accessible tissue: Callus, score: 45.75	N	N	N	N
vg0808817077	C -> A	LOC_Os08g14660-LOC_Os08g14670	intergenic_region ; MODIFIER	silent_mutation	Average:9.997; most accessible tissue: Callus, score: 45.75	N	N	N	N
vg0808817077	C -> DEL	N	N	silent_mutation	Average:9.997; most accessible tissue: Callus, score: 45.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808817077	4.60E-06	4.60E-06	mr1894	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