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Detailed information for vg0431405060:

Variant ID: vg0431405060 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31405060
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.10, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGTCCTTCAACGTTTGTTTCCAGAGCCTGGGAGGCTTCAGTTTATTTATGCTGATTTAGGCGATGCGAAAGCTGTATCCTTTTTCTCTACAATGTGAA[C/T]
TTTAATACCTTATTATAGCCATTTTTCCATACATTCATGTGTTGGTGTGATCTGTTTTGCACTTAACCAATAGCCAGGTTAACAAAATATTTTCAGAAAA

Reverse complement sequence

TTTTCTGAAAATATTTTGTTAACCTGGCTATTGGTTAAGTGCAAAACAGATCACACCAACACATGAATGTATGGAAAAATGGCTATAATAAGGTATTAAA[G/A]
TTCACATTGTAGAGAAAAAGGATACAGCTTTCGCATCGCCTAAATCAGCATAAATAAACTGAAGCCTCCCAGGCTCTGGAAACAAACGTTGAAGGACTCT

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	89.60%	10.10%	0.21%	0.04%	NA
All Indica	2759	85.20%	14.50%	0.29%	0.04%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	78.10%	21.20%	0.74%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	93.50%	6.20%	0.22%	0.00%	NA
Indica III	913	73.70%	25.70%	0.44%	0.11%	NA
Indica Intermediate	786	84.50%	15.10%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	0.00%	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
vg0431405060	C -> DEL	N	N	silent_mutation	Average:56.733; most accessible tissue: Callus, score: 79.969	N	N	N	N
vg0431405060	C -> T	LOC_Os04g52725.1	downstream_gene_variant ; 4873.0bp to feature; MODIFIER	silent_mutation	Average:56.733; most accessible tissue: Callus, score: 79.969	N	N	N	N
vg0431405060	C -> T	LOC_Os04g52740.1	downstream_gene_variant ; 2420.0bp to feature; MODIFIER	silent_mutation	Average:56.733; most accessible tissue: Callus, score: 79.969	N	N	N	N
vg0431405060	C -> T	LOC_Os04g52730.1	intron_variant ; MODIFIER	silent_mutation	Average:56.733; most accessible tissue: Callus, score: 79.969	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431405060	2.77E-06	NA	mr1138	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
vg0431405060	2.22E-06	3.29E-06	mr1138	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