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Detailed information for vg0432816051:

Variant ID: vg0432816051 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32816051
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.17, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

GCAATTGTATCGTTTACGTCGGCGTCGTTCAAGGCTGCATCAGTACATTCAACCTCTTGGATCGCTCTGGTTTGGATGATATATTTGCCTACCTATTTAT[C/T]
ATATGTCTCTATTAATCTAGTCTTAGCATATCAATTTAGCTCTATCGGCTGCTTCTCGTTTTAGGGTTTCTGCCGATATCGGCTAAATCGCGTTGCTAGA

Reverse complement sequence

TCTAGCAACGCGATTTAGCCGATATCGGCAGAAACCCTAAAACGAGAAGCAGCCGATAGAGCTAAATTGATATGCTAAGACTAGATTAATAGAGACATAT[G/A]
ATAAATAGGTAGGCAAATATATCATCCAAACCAGAGCGATCCAAGAGGTTGAATGTACTGATGCAGCCTTGAACGACGCCGACGTAAACGATACAATTGC

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	71.90%	28.00%	0.08%	0.00%	NA
All Indica	2759	97.10%	2.90%	0.07%	0.00%	NA
All Japonica	1512	28.50%	71.40%	0.07%	0.00%	NA
Aus	269	61.30%	38.30%	0.37%	0.00%	NA
Indica I	595	93.60%	6.20%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	14.20%	85.80%	0.00%	0.00%	NA
Tropical Japonica	504	38.90%	61.10%	0.00%	0.00%	NA
Japonica Intermediate	241	52.30%	47.30%	0.41%	0.00%	NA
VI/Aromatic	96	70.80%	29.20%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg0432816051	C -> T	LOC_Os04g55190.1	upstream_gene_variant ; 2896.0bp to feature; MODIFIER	silent_mutation	Average:23.844; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0432816051	C -> T	LOC_Os04g55200.1	upstream_gene_variant ; 2119.0bp to feature; MODIFIER	silent_mutation	Average:23.844; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0432816051	C -> T	LOC_Os04g55210.1	upstream_gene_variant ; 4595.0bp to feature; MODIFIER	silent_mutation	Average:23.844; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0432816051	C -> T	LOC_Os04g55190-LOC_Os04g55200	intergenic_region ; MODIFIER	silent_mutation	Average:23.844; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432816051	NA	3.06E-07	mr1040	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
vg0432816051	1.15E-06	1.73E-06	mr1758	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