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Detailed information for vg0817393582:

Variant ID: vg0817393582 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17393582
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CATTACCATCGGTTGCATTTGTCGTCGTCGACTATTTCCTGCATTTTCATGATTGGAGGATTTCGCCATTGTATTTGATGCACGTCTACGTCTTCATCGT[T/C]
GGCTTGTTTTCATCGCCACCGACTGATATTCTCGCCTTCACGGCTGGCTTATTATGTCGCCACTAATGGGCATTTTCATCTTCTTCACCAGCTGTCTCGT

Reverse complement sequence

ACGAGACAGCTGGTGAAGAAGATGAAAATGCCCATTAGTGGCGACATAATAAGCCAGCCGTGAAGGCGAGAATATCAGTCGGTGGCGATGAAAACAAGCC[A/G]
ACGATGAAGACGTAGACGTGCATCAAATACAATGGCGAAATCCTCCAATCATGAAAATGCAGGAAATAGTCGACGACGACAAATGCAACCGATGGTAATG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.90%	1.30%	6.37%	29.41%	NA
All Indica	2759	38.30%	2.20%	10.69%	48.79%	NA
All Japonica	1512	97.90%	0.00%	0.13%	1.98%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	55.10%	1.80%	5.21%	37.82%	NA
Indica II	465	34.60%	3.70%	11.18%	50.54%	NA
Indica III	913	30.90%	1.40%	12.60%	55.09%	NA
Indica Intermediate	786	36.30%	2.70%	12.34%	48.73%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	94.80%	0.00%	0.40%	4.76%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	1.10%	4.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817393582	T -> C	LOC_Os08g28500.1	upstream_gene_variant ; 3561.0bp to feature; MODIFIER	silent_mutation	Average:17.714; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0817393582	T -> C	LOC_Os08g28490.1	downstream_gene_variant ; 1216.0bp to feature; MODIFIER	silent_mutation	Average:17.714; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0817393582	T -> C	LOC_Os08g28490-LOC_Os08g28500	intergenic_region ; MODIFIER	silent_mutation	Average:17.714; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0817393582	T -> DEL	N	N	silent_mutation	Average:17.714; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817393582	4.60E-06	NA	mr1695	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
vg0817393582	2.41E-06	NA	mr1695	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