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Detailed information for vg1200750451:

Variant ID: vg1200750451 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 750451
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.13, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATCAAATTTAGTCCTGCATGTTTGTGTATATACTTATATCATCACAAACAATCTTACTATTTTTTTAATTTTTTTCTACAACTATTTAAGTCGCATG[C/T]
GAATGATGGGTGCCATAGCACCTAGGTGTAGAAAATCCTTGTCCGTTCTCACCATATCTGGCTTATTCCTCAAATAAGCCAAACGGTATATTTGCATAAA

Reverse complement sequence

TTTATGCAAATATACCGTTTGGCTTATTTGAGGAATAAGCCAGATATGGTGAGAACGGACAAGGATTTTCTACACCTAGGTGCTATGGCACCCATCATTC[G/A]
CATGCGACTTAAATAGTTGTAGAAAAAAATTAAAAAAATAGTAAGATTGTTTGTGATGATATAAGTATATACACAAACATGCAGGACTAAATTTGATCTA

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	53.40%	46.30%	0.30%	0.00%	NA
All Indica	2759	23.60%	75.90%	0.47%	0.00%	NA
All Japonica	1512	95.90%	4.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	43.00%	56.50%	0.50%	0.00%	NA
Indica II	465	8.80%	91.00%	0.22%	0.00%	NA
Indica III	913	17.90%	82.10%	0.00%	0.00%	NA
Indica Intermediate	786	24.40%	74.40%	1.15%	0.00%	NA
Temperate Japonica	767	93.90%	6.10%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	27.80%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200750451	C -> T	LOC_Os12g02330.2	downstream_gene_variant ; 3151.0bp to feature; MODIFIER	silent_mutation	Average:34.318; most accessible tissue: Callus, score: 56.813	N	N	N	N
vg1200750451	C -> T	LOC_Os12g02330-LOC_Os12g02340	intergenic_region ; MODIFIER	silent_mutation	Average:34.318; most accessible tissue: Callus, score: 56.813	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200750451	NA	9.13E-10	mr1151	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
vg1200750451	NA	3.62E-09	mr1174	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
vg1200750451	2.18E-06	2.18E-06	mr1545	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