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Detailed information for vg1217795376:

Variant ID: vg1217795376 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17795376
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTGCTAATAGCAGTTATGCGTGGTTTATGGGCTTAACTGACCTCCAAACCATCAATACAATGTTATATAAGGAGGAAAAGCTCTCACTCTCAATTGA[C/T]
ACAGCAAAGTGGAGTACAACTCACTTTCATACTTACATATTGCTCTAGTAGAATAGGAAGAGAGTGAGGGGAAGCTTCAAAAGGAGTGTCGGAAATGTCG

Reverse complement sequence

CGACATTTCCGACACTCCTTTTGAAGCTTCCCCTCACTCTCTTCCTATTCTACTAGAGCAATATGTAAGTATGAAAGTGAGTTGTACTCCACTTTGCTGT[G/A]
TCAATTGAGAGTGAGAGCTTTTCCTCCTTATATAACATTGTATTGATGGTTTGGAGGTCAGTTAAGCCCATAAACCACGCATAACTGCTATTAGCACTTC

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	53.00%	14.30%	0.76%	31.97%	NA
All Indica	2759	43.80%	23.70%	1.09%	31.39%	NA
All Japonica	1512	69.20%	0.40%	0.33%	30.09%	NA
Aus	269	60.60%	0.70%	0.00%	38.66%	NA
Indica I	595	61.70%	36.10%	0.34%	1.85%	NA
Indica II	465	26.70%	14.80%	1.94%	56.56%	NA
Indica III	913	41.90%	16.10%	0.77%	41.18%	NA
Indica Intermediate	786	42.50%	28.50%	1.53%	27.48%	NA
Temperate Japonica	767	95.70%	0.40%	0.00%	3.91%	NA
Tropical Japonica	504	39.90%	0.20%	0.99%	58.93%	NA
Japonica Intermediate	241	46.10%	0.80%	0.00%	53.11%	NA
VI/Aromatic	96	36.50%	1.00%	0.00%	62.50%	NA
Intermediate	90	56.70%	13.30%	1.11%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217795376	C -> DEL	N	N	silent_mutation	Average:42.37; most accessible tissue: Callus, score: 88.92	N	N	N	N
vg1217795376	C -> T	LOC_Os12g29760.1	upstream_gene_variant ; 4265.0bp to feature; MODIFIER	silent_mutation	Average:42.37; most accessible tissue: Callus, score: 88.92	N	N	N	N
vg1217795376	C -> T	LOC_Os12g29760.2	upstream_gene_variant ; 4265.0bp to feature; MODIFIER	silent_mutation	Average:42.37; most accessible tissue: Callus, score: 88.92	N	N	N	N
vg1217795376	C -> T	LOC_Os12g29760-LOC_Os12g29780	intergenic_region ; MODIFIER	silent_mutation	Average:42.37; most accessible tissue: Callus, score: 88.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217795376	NA	1.90E-07	mr1180	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
vg1217795376	NA	1.15E-06	mr1336	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
vg1217795376	NA	3.59E-08	mr1579	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