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Detailed information for vg0814576026:

Variant ID: vg0814576026 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14576026
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AACCGAAAATTTGCCAAGGAATCTTACTAAATTTGGCGTTAACACAACATCAACACTCTGCTACAACAGGGTCCTTTCAACCTAGTAACCCACCTTGATG[C/T]
GGATGCGTGGTTATATAAGTTGAAACGACTATCCCCAAGTCTAATATATTTCATTTTGGGAGTTTTTGGGTTAATCATGATTGGTTTCTAGAGCAGGTCA

Reverse complement sequence

TGACCTGCTCTAGAAACCAATCATGATTAACCCAAAAACTCCCAAAATGAAATATATTAGACTTGGGGATAGTCGTTTCAACTTATATAACCACGCATCC[G/A]
CATCAAGGTGGGTTACTAGGTTGAAAGGACCCTGTTGTAGCAGAGTGTTGATGTTGTGTTAACGCCAAATTTAGTAAGATTCCTTGGCAAATTTTCGGTT

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	37.70%	13.30%	1.59%	47.36%	NA
All Indica	2759	19.00%	0.30%	2.50%	78.22%	NA
All Japonica	1512	58.30%	40.20%	0.13%	1.39%	NA
Aus	269	87.40%	0.00%	1.49%	11.15%	NA
Indica I	595	7.60%	0.20%	3.03%	89.24%	NA
Indica II	465	14.80%	0.20%	4.09%	80.86%	NA
Indica III	913	24.60%	0.40%	1.75%	73.17%	NA
Indica Intermediate	786	23.50%	0.30%	2.04%	74.17%	NA
Temperate Japonica	767	45.10%	52.90%	0.26%	1.69%	NA
Tropical Japonica	504	72.60%	26.60%	0.00%	0.79%	NA
Japonica Intermediate	241	70.10%	28.20%	0.00%	1.66%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	56.70%	13.30%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814576026	C -> T	LOC_Os08g24130.1	upstream_gene_variant ; 1760.0bp to feature; MODIFIER	silent_mutation	Average:10.763; most accessible tissue: Callus, score: 65.33	N	N	N	N
vg0814576026	C -> T	LOC_Os08g24140.1	downstream_gene_variant ; 4070.0bp to feature; MODIFIER	silent_mutation	Average:10.763; most accessible tissue: Callus, score: 65.33	N	N	N	N
vg0814576026	C -> T	LOC_Os08g24130-LOC_Os08g24140	intergenic_region ; MODIFIER	silent_mutation	Average:10.763; most accessible tissue: Callus, score: 65.33	N	N	N	N
vg0814576026	C -> DEL	N	N	silent_mutation	Average:10.763; most accessible tissue: Callus, score: 65.33	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814576026	NA	7.40E-07	mr1708	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
vg0814576026	8.77E-06	2.67E-07	mr1708	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
vg0814576026	4.40E-06	NA	mr1182_2	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
vg0814576026	2.85E-06	2.64E-11	mr1282_2	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