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Detailed information for vg0431094486:

Variant ID: vg0431094486 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31094486
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

TCATATTTGCAAACAAAAAATAATTTGTGAATAAAACTTTTATATACGTGTTCTTAGTGATCTAAAAGCAAATGCTGAAAAATAAATTACGATGAGAAAA[C/T]
CCAAAAATCAACACCAAATTTAAGGTGGAAAATTTAAATTTTGGCTGATAAATATAAGCATAAAGAAAAGATGAGGCCCGTCCTGTGGAATTCAGTGTAG

Reverse complement sequence

CTACACTGAATTCCACAGGACGGGCCTCATCTTTTCTTTATGCTTATATTTATCAGCCAAAATTTAAATTTTCCACCTTAAATTTGGTGTTGATTTTTGG[G/A]
TTTTCTCATCGTAATTTATTTTTCAGCATTTGCTTTTAGATCACTAAGAACACGTATATAAAAGTTTTATTCACAAATTATTTTTTGTTTGCAAATATGA

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	59.10%	40.60%	0.19%	0.06%	NA
All Indica	2759	90.90%	8.80%	0.29%	0.07%	NA
All Japonica	1512	5.00%	94.90%	0.07%	0.07%	NA
Aus	269	30.90%	69.10%	0.00%	0.00%	NA
Indica I	595	81.00%	18.50%	0.34%	0.17%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	96.80%	2.80%	0.22%	0.11%	NA
Indica Intermediate	786	89.30%	10.20%	0.51%	0.00%	NA
Temperate Japonica	767	2.90%	97.10%	0.00%	0.00%	NA
Tropical Japonica	504	5.80%	94.20%	0.00%	0.00%	NA
Japonica Intermediate	241	10.00%	89.20%	0.41%	0.41%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	60.00%	40.00%	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
vg0431094486	C -> DEL	N	N	silent_mutation	Average:50.475; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg0431094486	C -> T	LOC_Os04g52320.1	downstream_gene_variant ; 1629.0bp to feature; MODIFIER	silent_mutation	Average:50.475; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg0431094486	C -> T	LOC_Os04g52330.1	downstream_gene_variant ; 1112.0bp to feature; MODIFIER	silent_mutation	Average:50.475; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg0431094486	C -> T	LOC_Os04g52340.1	downstream_gene_variant ; 3988.0bp to feature; MODIFIER	silent_mutation	Average:50.475; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg0431094486	C -> T	LOC_Os04g52320-LOC_Os04g52330	intergenic_region ; MODIFIER	silent_mutation	Average:50.475; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431094486	NA	4.70E-11	mr1011_2	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
vg0431094486	NA	3.92E-06	mr1011_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
vg0431094486	NA	4.21E-06	mr1015_2	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
vg0431094486	NA	4.33E-06	mr1031_2	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
vg0431094486	NA	2.46E-09	mr1172_2	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
vg0431094486	NA	1.31E-06	mr1522_2	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
vg0431094486	NA	6.42E-06	mr1524_2	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
vg0431094486	NA	1.07E-21	mr1627_2	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
vg0431094486	NA	6.55E-08	mr1683_2	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
vg0431094486	NA	4.38E-20	mr1922_2	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