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Detailed information for vg0314687874:

Variant ID: vg0314687874 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14687874
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, A: 0.16, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAGCATATGCCTAGCCAAATTGATGCACCAAAATACAAATTGTCAAGTTCTTGTAGTAGAACGCACCTACCTGTCAAGTTGTTACACTTGGACGCTCA[T/A]
TTCTCAAGTTCTTGCACTATATCGCACCCACCTGCCAAGTTGTACCGTGGGTGCAATTTACTCTTCTTTCTTCTACAGATTTTTGGAAGCCAACCTTGCA

Reverse complement sequence

TGCAAGGTTGGCTTCCAAAAATCTGTAGAAGAAAGAAGAGTAAATTGCACCCACGGTACAACTTGGCAGGTGGGTGCGATATAGTGCAAGAACTTGAGAA[A/T]
TGAGCGTCCAAGTGTAACAACTTGACAGGTAGGTGCGTTCTACTACAAGAACTTGACAATTTGTATTTTGGTGCATCAATTTGGCTAGGCATATGCTAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	43.90%	29.70%	0.55%	25.84%	NA
All Indica	2759	16.20%	49.50%	0.47%	33.82%	NA
All Japonica	1512	98.70%	0.10%	0.00%	1.12%	NA
Aus	269	2.20%	3.00%	4.46%	90.33%	NA
Indica I	595	7.90%	55.50%	0.34%	36.30%	NA
Indica II	465	7.50%	22.40%	1.72%	68.39%	NA
Indica III	913	24.90%	62.90%	0.00%	12.27%	NA
Indica Intermediate	786	17.40%	45.70%	0.38%	36.51%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	97.60%	0.20%	0.00%	2.18%	NA
Japonica Intermediate	241	97.90%	0.40%	0.00%	1.66%	NA
VI/Aromatic	96	87.50%	5.20%	0.00%	7.29%	NA
Intermediate	90	51.10%	24.40%	1.11%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314687874	T -> A	LOC_Os03g25660.1	downstream_gene_variant ; 2482.0bp to feature; MODIFIER	silent_mutation	Average:54.683; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0314687874	T -> A	LOC_Os03g25650.1	intron_variant ; MODIFIER	silent_mutation	Average:54.683; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg0314687874	T -> DEL	N	N	silent_mutation	Average:54.683; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314687874	NA	5.08E-07	mr1104	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
vg0314687874	NA	2.95E-07	mr1245	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
vg0314687874	NA	2.27E-07	mr1690	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
vg0314687874	NA	1.40E-07	mr1212_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
vg0314687874	NA	2.32E-12	mr1216_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
vg0314687874	2.33E-06	NA	mr1542_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