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Detailed information for vg0817256964:

Variant ID: vg0817256964 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17256964
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGGAAGGTTTTTATGCTATACGTCCATAAAAACATTGTCTGGATATCCTTCAATCTCCAAATAACTCTGTCACTATATACAACATGCGTATAGCTTGT[G/T]
CATGGATGCAAAAATGATAGCAGGGCTCTTATTTTCATCGAGCAAATGATGGCCTGCTCCTTTCGATCAACCTTGAGCTTCCTTTCGAGATTAGGATATC

Reverse complement sequence

GATATCCTAATCTCGAAAGGAAGCTCAAGGTTGATCGAAAGGAGCAGGCCATCATTTGCTCGATGAAAATAAGAGCCCTGCTATCATTTTTGCATCCATG[C/A]
ACAAGCTATACGCATGTTGTATATAGTGACAGAGTTATTTGGAGATTGAAGGATATCCAGACAATGTTTTTATGGACGTATAGCATAAAAACCTTCCAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	1.70%	0.78%	5.42%	NA
All Indica	2759	92.80%	0.00%	0.51%	6.71%	NA
All Japonica	1512	88.80%	5.20%	1.52%	4.43%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	98.00%	0.00%	0.17%	1.85%	NA
Indica II	465	98.90%	0.20%	0.00%	0.86%	NA
Indica III	913	85.90%	0.00%	1.20%	12.92%	NA
Indica Intermediate	786	93.10%	0.00%	0.25%	6.62%	NA
Temperate Japonica	767	99.00%	0.80%	0.26%	0.00%	NA
Tropical Japonica	504	73.20%	11.10%	2.98%	12.70%	NA
Japonica Intermediate	241	89.20%	7.10%	2.49%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817256964	G -> T	LOC_Os08g28270.1	downstream_gene_variant ; 746.0bp to feature; MODIFIER	silent_mutation	Average:57.876; most accessible tissue: Callus, score: 80.355	N	N	N	N
vg0817256964	G -> T	LOC_Os08g28260-LOC_Os08g28270	intergenic_region ; MODIFIER	silent_mutation	Average:57.876; most accessible tissue: Callus, score: 80.355	N	N	N	N
vg0817256964	G -> DEL	N	N	silent_mutation	Average:57.876; most accessible tissue: Callus, score: 80.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817256964	NA	7.46E-06	mr1236	Jap_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
vg0817256964	NA	2.35E-07	mr1951	Jap_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
vg0817256964	5.54E-07	6.25E-07	mr1037_2	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
vg0817256964	NA	7.73E-08	mr1676_2	Jap_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