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Detailed information for vg1214525892:

Variant ID: vg1214525892 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14525892
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGAATAAAATGTCATTACAGAGGTAGATAGTTCCTCTCAATCAATAAAGTTCTGAGCAGTGGAAAAAAAAAAGAAATAGCGCAGGCGACTCCTCTCCA[T/C]
AGGCAGCTTGACCAGGGCTACGCCTAATCATCCACACCATCAGCATCACTGTAGAACTCCTCCTCTGATGAATGATTGCAAGGTGAGTATATGACATACT

Reverse complement sequence

AGTATGTCATATACTCACCTTGCAATCATTCATCAGAGGAGGAGTTCTACAGTGATGCTGATGGTGTGGATGATTAGGCGTAGCCCTGGTCAAGCTGCCT[A/G]
TGGAGAGGAGTCGCCTGCGCTATTTCTTTTTTTTTTCCACTGCTCAGAACTTTATTGATTGAGAGGAACTATCTACCTCTGTAATGACATTTTATTCGCT

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	65.80%	26.00%	6.62%	1.54%	NA
All Indica	2759	73.30%	25.10%	1.56%	0.07%	NA
All Japonica	1512	66.50%	13.10%	16.07%	4.37%	NA
Aus	269	4.10%	89.20%	5.20%	1.49%	NA
Indica I	595	67.20%	32.40%	0.34%	0.00%	NA
Indica II	465	72.70%	23.70%	3.44%	0.22%	NA
Indica III	913	78.20%	20.60%	1.20%	0.00%	NA
Indica Intermediate	786	72.40%	25.70%	1.78%	0.13%	NA
Temperate Japonica	767	85.00%	4.60%	6.78%	3.65%	NA
Tropical Japonica	504	43.10%	23.60%	27.18%	6.15%	NA
Japonica Intermediate	241	56.40%	18.30%	22.41%	2.90%	NA
VI/Aromatic	96	14.60%	78.10%	7.29%	0.00%	NA
Intermediate	90	67.80%	24.40%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214525892	T -> C	LOC_Os12g25250-LOC_Os12g25260	intergenic_region ; MODIFIER	silent_mutation	Average:27.23; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1214525892	T -> DEL	N	N	silent_mutation	Average:27.23; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214525892	NA	8.00E-07	mr1057	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
vg1214525892	NA	4.01E-06	mr1657	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
vg1214525892	3.45E-06	NA	mr1739_2	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