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Detailed information for vg0817461830:

Variant ID: vg0817461830 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17461830
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, G: 0.19, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCTGGCCAAGCTATAAACATGGCACACCCTGTGTGTATGGTTGAAAGCGAGTCAAAATTTGACTCACTTACGTGTAACACGTTGGCTGTTGTCGCGTG[C/G]
GATGGTTGTATAGAAAGTAAACTTTTGACTCGCGATGTCAAGTTGTGTGGGGAGAGTGAGAAATGCTCAGATGGCGCGTGGGTGGTAACGGAGGGATTGT

Reverse complement sequence

ACAATCCCTCCGTTACCACCCACGCGCCATCTGAGCATTTCTCACTCTCCCCACACAACTTGACATCGCGAGTCAAAAGTTTACTTTCTATACAACCATC[G/C]
CACGCGACAACAGCCAACGTGTTACACGTAAGTGAGTCAAATTTTGACTCGCTTTCAACCATACACACAGGGTGTGCCATGTTTATAGCTTGGCCAGCCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.20%	11.20%	0.49%	44.10%	NA
All Indica	2759	18.80%	16.70%	0.69%	63.72%	NA
All Japonica	1512	82.70%	3.90%	0.26%	13.16%	NA
Aus	269	65.80%	0.00%	0.00%	34.20%	NA
Indica I	595	22.50%	36.00%	0.00%	41.51%	NA
Indica II	465	17.80%	4.50%	1.29%	76.34%	NA
Indica III	913	15.70%	12.90%	0.55%	70.87%	NA
Indica Intermediate	786	20.40%	13.90%	1.02%	64.76%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	58.30%	8.30%	0.40%	32.94%	NA
Japonica Intermediate	241	82.60%	7.10%	0.41%	9.96%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	64.40%	7.80%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817461830	C -> G	LOC_Os08g28580.1	downstream_gene_variant ; 3408.0bp to feature; MODIFIER	silent_mutation	Average:14.42; most accessible tissue: Callus, score: 91.581	N	N	N	N
vg0817461830	C -> G	LOC_Os08g28590.1	downstream_gene_variant ; 427.0bp to feature; MODIFIER	silent_mutation	Average:14.42; most accessible tissue: Callus, score: 91.581	N	N	N	N
vg0817461830	C -> G	LOC_Os08g28590-LOC_Os08g28600	intergenic_region ; MODIFIER	silent_mutation	Average:14.42; most accessible tissue: Callus, score: 91.581	N	N	N	N
vg0817461830	C -> DEL	N	N	silent_mutation	Average:14.42; most accessible tissue: Callus, score: 91.581	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817461830	4.92E-06	4.92E-06	mr1881	Jap_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