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Detailed information for vg0808212491:

Variant ID: vg0808212491 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8212491
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: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCTGTAGGATTGATCGATCATCTAGAGCTAATCTTCCATTTTATAAAAGATAATCAATGATCCCTTCCATATATTTATACAAGCTTTTATATTTGGAA[T/C]
ATGGCATTTGTGAGGGGTATGCGTACATGATGTACATCACGTACACCGGCTGGGCTGGAGCATAGGCAACCAGTACTATACAAGTGTCATATAATATTCA

Reverse complement sequence

TGAATATTATATGACACTTGTATAGTACTGGTTGCCTATGCTCCAGCCCAGCCGGTGTACGTGATGTACATCATGTACGCATACCCCTCACAAATGCCAT[A/G]
TTCCAAATATAAAAGCTTGTATAAATATATGGAAGGGATCATTGATTATCTTTTATAAAATGGAAGATTAGCTCTAGATGATCGATCAATCCTACAGCTA

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	40.80%	4.70%	1.33%	53.22%	NA
All Indica	2759	12.60%	5.50%	1.92%	79.96%	NA
All Japonica	1512	85.70%	0.30%	0.20%	13.76%	NA
Aus	269	55.80%	22.30%	1.49%	20.45%	NA
Indica I	595	10.80%	0.70%	1.85%	86.72%	NA
Indica II	465	9.50%	14.20%	2.37%	73.98%	NA
Indica III	913	9.70%	4.40%	0.88%	84.99%	NA
Indica Intermediate	786	19.10%	5.50%	2.93%	72.52%	NA
Temperate Japonica	767	95.00%	0.30%	0.00%	4.69%	NA
Tropical Japonica	504	81.70%	0.40%	0.60%	17.26%	NA
Japonica Intermediate	241	64.30%	0.40%	0.00%	35.27%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	43.30%	4.40%	3.33%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808212491	T -> C	LOC_Os08g13770.1	upstream_gene_variant ; 2520.0bp to feature; MODIFIER	silent_mutation	Average:13.707; most accessible tissue: Callus, score: 92.29	N	N	N	N
vg0808212491	T -> C	LOC_Os08g13780.1	upstream_gene_variant ; 3936.0bp to feature; MODIFIER	silent_mutation	Average:13.707; most accessible tissue: Callus, score: 92.29	N	N	N	N
vg0808212491	T -> C	LOC_Os08g13770-LOC_Os08g13780	intergenic_region ; MODIFIER	silent_mutation	Average:13.707; most accessible tissue: Callus, score: 92.29	N	N	N	N
vg0808212491	T -> DEL	N	N	silent_mutation	Average:13.707; most accessible tissue: Callus, score: 92.29	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808212491	5.53E-08	8.20E-12	mr1188	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
vg0808212491	NA	2.58E-08	mr1188_2	Ind_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