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Detailed information for vg0114116382:

Variant ID: vg0114116382 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14116382
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

CTGAATTTGCTATGAAAAGAAGTAGCTCAACTTCCGTGAGCCTGATCCATTAAATTTGTGCTTTGCTTCCTCTTTACCCAAGCTAATGTAATGTGAATAG[A/G]
CCCATCTTGTTGGAATTCTACGTGAAACCCATTCCAGCAATCCAGTCCACGAAGGCTTCCTCTTGCGAGTCATCACGGCGGCGAGCGGGTGGCGGTGGCG

Reverse complement sequence

CGCCACCGCCACCCGCTCGCCGCCGTGATGACTCGCAAGAGGAAGCCTTCGTGGACTGGATTGCTGGAATGGGTTTCACGTAGAATTCCAACAAGATGGG[T/C]
CTATTCACATTACATTAGCTTGGGTAAAGAGGAAGCAAAGCACAAATTTAATGGATCAGGCTCACGGAAGTTGAGCTACTTCTTTTCATAGCAAATTCAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.30%	7.30%	1.90%	17.50%	NA
All Indica	2759	64.20%	8.50%	1.78%	25.55%	NA
All Japonica	1512	95.30%	4.60%	0.00%	0.13%	NA
Aus	269	44.60%	1.10%	14.13%	40.15%	NA
Indica I	595	29.60%	13.60%	1.68%	55.13%	NA
Indica II	465	59.40%	13.30%	0.43%	26.88%	NA
Indica III	913	93.30%	1.30%	1.10%	4.27%	NA
Indica Intermediate	786	59.40%	10.10%	3.44%	27.10%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	89.30%	10.50%	0.00%	0.20%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	60.40%	38.50%	0.00%	1.04%	NA
Intermediate	90	82.20%	2.20%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114116382	A -> G	LOC_Os01g25020.1	downstream_gene_variant ; 2089.0bp to feature; MODIFIER	silent_mutation	Average:22.058; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0114116382	A -> G	LOC_Os01g25030.1	downstream_gene_variant ; 616.0bp to feature; MODIFIER	silent_mutation	Average:22.058; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0114116382	A -> G	LOC_Os01g25020-LOC_Os01g25030	intergenic_region ; MODIFIER	silent_mutation	Average:22.058; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0114116382	A -> DEL	N	N	silent_mutation	Average:22.058; 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
vg0114116382	1.58E-06	1.33E-08	mr1064	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
vg0114116382	NA	6.07E-06	mr1125	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
vg0114116382	NA	4.50E-08	mr1136	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
vg0114116382	NA	2.02E-07	mr1458	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
vg0114116382	NA	2.77E-06	mr1534	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
vg0114116382	NA	5.89E-06	mr1679	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
vg0114116382	2.79E-07	6.11E-09	mr1741	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
vg0114116382	NA	3.29E-07	mr1458_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