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Detailed information for vg1223180692:

Variant ID: vg1223180692 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23180692
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: 0.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GTTATTTGGGCCATTTGGAAAACTAGAAATAAAGTATGCTTTGAGAAACAATATCCACGTGTTCCCATTGATTTGGTCTTTTTGGCATATGCCACTAGGG[C/T]
CTAGTTTAGTTCCTAACTTTTTCTTCAAACTTTCAAATTTTTCATCACATCAAAACTTTCCTACACACACAAACTTTTAACTTTTCCGTCATATCTGTCC

Reverse complement sequence

GGACAGATATGACGGAAAAGTTAAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAATTTGAAAGTTTGAAGAAAAAGTTAGGAACTAAACTAG[G/A]
CCCTAGTGGCATATGCCAAAAAGACCAAATCAATGGGAACACGTGGATATTGTTTCTCAAAGCATACTTTATTTCTAGTTTTCCAAATGGCCCAAATAAC

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	91.70%	3.40%	0.04%	4.87%	NA
All Indica	2759	86.40%	5.70%	0.07%	7.90%	NA
All Japonica	1512	99.50%	0.00%	0.00%	0.53%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	79.30%	6.90%	0.00%	13.78%	NA
Indica II	465	82.80%	0.00%	0.22%	16.99%	NA
Indica III	913	95.20%	4.60%	0.00%	0.22%	NA
Indica Intermediate	786	83.60%	9.30%	0.13%	7.00%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	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
vg1223180692	C -> DEL	N	N	silent_mutation	Average:46.433; most accessible tissue: Callus, score: 80.933	N	N	N	N
vg1223180692	C -> T	LOC_Os12g37760.1	upstream_gene_variant ; 1871.0bp to feature; MODIFIER	silent_mutation	Average:46.433; most accessible tissue: Callus, score: 80.933	N	N	N	N
vg1223180692	C -> T	LOC_Os12g37750.1	downstream_gene_variant ; 4853.0bp to feature; MODIFIER	silent_mutation	Average:46.433; most accessible tissue: Callus, score: 80.933	N	N	N	N
vg1223180692	C -> T	LOC_Os12g37750-LOC_Os12g37760	intergenic_region ; MODIFIER	silent_mutation	Average:46.433; most accessible tissue: Callus, score: 80.933	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223180692	NA	2.18E-07	mr1707	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
vg1223180692	2.13E-06	5.20E-09	mr1707_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