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Detailed information for vg0314985097:

Variant ID: vg0314985097 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14985097
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAAAAAATAAAAGATAAAGTAACTTCTAATCATTATATTAATAAATTACTCTCTTTGTTCCTGATATTTGACGTCGTTGACTTTTTTTAAATATGTTT[A/G]
ACCGTTCGTCTTATTAAAAAATTAAGTAATTATTAATTCTTTTTCTATCATTTGATTCATTGTTAAATATATACTTTTATGTATACATATAGTTTTACAT

Reverse complement sequence

ATGTAAAACTATATGTATACATAAAAGTATATATTTAACAATGAATCAAATGATAGAAAAAGAATTAATAATTACTTAATTTTTTAATAAGACGAACGGT[T/C]
AAACATATTTAAAAAAAGTCAACGACGTCAAATATCAGGAACAAAGAGAGTAATTTATTAATATAATGATTAGAAGTTACTTTATCTTTTATTTTTTTCA

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	50.80%	0.30%	2.92%	46.00%	NA
All Indica	2759	29.60%	0.40%	4.35%	65.60%	NA
All Japonica	1512	79.00%	0.10%	1.12%	19.78%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	50.30%	0.20%	1.51%	48.07%	NA
Indica II	465	43.40%	0.40%	4.73%	51.40%	NA
Indica III	913	14.60%	0.40%	6.02%	78.97%	NA
Indica Intermediate	786	23.40%	0.50%	4.33%	71.76%	NA
Temperate Japonica	767	96.30%	0.00%	0.00%	3.65%	NA
Tropical Japonica	504	53.80%	0.20%	2.98%	43.06%	NA
Japonica Intermediate	241	76.30%	0.40%	0.83%	22.41%	NA
VI/Aromatic	96	66.70%	0.00%	0.00%	33.33%	NA
Intermediate	90	65.60%	0.00%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0314985097	A -> DEL	N	N	silent_mutation	Average:18.942; most accessible tissue: Callus, score: 25.377	N	N	N	N
vg0314985097	A -> G	LOC_Os03g26180.1	downstream_gene_variant ; 3313.0bp to feature; MODIFIER	silent_mutation	Average:18.942; most accessible tissue: Callus, score: 25.377	N	N	N	N
vg0314985097	A -> G	LOC_Os03g26130-LOC_Os03g26180	intergenic_region ; MODIFIER	silent_mutation	Average:18.942; most accessible tissue: Callus, score: 25.377	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314985097	NA	3.52E-06	mr1088	Jap_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
vg0314985097	NA	6.83E-06	mr1437	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
vg0314985097	NA	9.24E-06	mr1502	Jap_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
vg0314985097	NA	1.31E-06	mr1620	Jap_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
vg0314985097	4.59E-06	9.95E-06	mr1671	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
vg0314985097	NA	1.02E-06	mr1422_2	Jap_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