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Detailed information for vg0821985309:

Variant ID: vg0821985309 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21985309
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATATGATTTTTTAAAACAACTTTCCTATATAAATCTTTTACAAAAAATGCATCGTTTAGTAGTTTGGGAAGCGTGCGCGCGGATAACGAAACAAACT[C/T]
ACTCACTATCTCACCCTCTCAAACGCAGCCTAAAATTGTTTTCCTTTTTTTAATTCGCTATTCTTTTCTTTCTTACTGTAAATTTTAGTAAATACATGGA

Reverse complement sequence

TCCATGTATTTACTAAAATTTACAGTAAGAAAGAAAAGAATAGCGAATTAAAAAAAGGAAAACAATTTTAGGCTGCGTTTGAGAGGGTGAGATAGTGAGT[G/A]
AGTTTGTTTCGTTATCCGCGCGCACGCTTCCCAAACTACTAAACGATGCATTTTTTGTAAAAGATTTATATAGGAAAGTTGTTTTAAAAAATCATATTAG

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	51.70%	1.20%	13.99%	33.09%	NA
All Indica	2759	35.60%	1.40%	16.78%	46.25%	NA
All Japonica	1512	87.40%	0.00%	4.83%	7.74%	NA
Aus	269	17.50%	7.10%	31.23%	44.24%	NA
Indica I	595	13.90%	0.30%	18.49%	67.23%	NA
Indica II	465	52.70%	3.20%	21.94%	22.15%	NA
Indica III	913	35.90%	1.10%	11.39%	51.59%	NA
Indica Intermediate	786	41.50%	1.40%	18.70%	38.42%	NA
Temperate Japonica	767	96.60%	0.00%	2.74%	0.65%	NA
Tropical Japonica	504	73.20%	0.00%	8.93%	17.86%	NA
Japonica Intermediate	241	88.00%	0.00%	2.90%	9.13%	NA
VI/Aromatic	96	43.80%	0.00%	26.04%	30.21%	NA
Intermediate	90	56.70%	0.00%	17.78%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0821985309	C -> T	LOC_Os08g34910.1	upstream_gene_variant ; 1255.0bp to feature; MODIFIER	silent_mutation	Average:27.903; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0821985309	C -> T	LOC_Os08g34920.1	upstream_gene_variant ; 1864.0bp to feature; MODIFIER	silent_mutation	Average:27.903; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0821985309	C -> T	LOC_Os08g34900.1	downstream_gene_variant ; 2952.0bp to feature; MODIFIER	silent_mutation	Average:27.903; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0821985309	C -> T	LOC_Os08g34910-LOC_Os08g34920	intergenic_region ; MODIFIER	silent_mutation	Average:27.903; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0821985309	C -> DEL	N	N	silent_mutation	Average:27.903; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821985309	1.20E-06	1.09E-07	mr1758	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