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Detailed information for vg0112184246:

Variant ID: vg0112184246 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 12184246
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTAATACAAATAGTTTTGAAAAATTCTGAACGTAGAGTATATATAGTGGTATCTATCGGTCTATCGATCAAAAATCAAGTTCAAATTTAACTACACAT[C/T]
GGGGAGTGGGGCTTTCATCTGGGAAGCAGATGGGCCCAGGCATGGATGCAGCCTCTAAGGAGGAAATTTGGCACCTCCATGTGCTCCTATATATTTGGCA

Reverse complement sequence

TGCCAAATATATAGGAGCACATGGAGGTGCCAAATTTCCTCCTTAGAGGCTGCATCCATGCCTGGGCCCATCTGCTTCCCAGATGAAAGCCCCACTCCCC[G/A]
ATGTGTAGTTAAATTTGAACTTGATTTTTGATCGATAGACCGATAGATACCACTATATATACTCTACGTTCAGAATTTTTCAAAACTATTTGTATTAAAT

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	47.50%	47.30%	0.44%	4.76%	NA
All Indica	2759	30.60%	67.70%	0.22%	1.49%	NA
All Japonica	1512	82.20%	5.00%	0.79%	12.04%	NA
Aus	269	31.20%	68.80%	0.00%	0.00%	NA
Indica I	595	9.70%	90.30%	0.00%	0.00%	NA
Indica II	465	21.30%	75.70%	0.00%	3.01%	NA
Indica III	913	42.80%	56.10%	0.44%	0.66%	NA
Indica Intermediate	786	37.80%	59.30%	0.25%	2.67%	NA
Temperate Japonica	767	88.90%	1.30%	0.65%	9.13%	NA
Tropical Japonica	504	66.90%	11.90%	1.39%	19.84%	NA
Japonica Intermediate	241	92.90%	2.10%	0.00%	4.98%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	53.30%	41.10%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0112184246	C -> T	LOC_Os01g21710.1	upstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:57.045; most accessible tissue: Callus, score: 70.314	N	N	N	N
vg0112184246	C -> T	LOC_Os01g21720.1	downstream_gene_variant ; 3704.0bp to feature; MODIFIER	silent_mutation	Average:57.045; most accessible tissue: Callus, score: 70.314	N	N	N	N
vg0112184246	C -> T	LOC_Os01g21700-LOC_Os01g21710	intergenic_region ; MODIFIER	silent_mutation	Average:57.045; most accessible tissue: Callus, score: 70.314	N	N	N	N
vg0112184246	C -> DEL	N	N	silent_mutation	Average:57.045; most accessible tissue: Callus, score: 70.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0112184246	4.73E-06	NA	mr1613	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
vg0112184246	9.06E-06	3.96E-08	mr1613	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
vg0112184246	NA	4.19E-06	mr1619	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