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Detailed information for vg0314601404:

Variant ID: vg0314601404 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14601404
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAAAATGATGTAGAGCCTATAAAAAAACGTTATCCAGTATAGGAGAGAACTTGTTATCTTCAAACTTTATTCAAACTTTATGACAACAATTAGATAA[G/A]
AACAAACAAAATAAAAACATTGCACCGATAGAAGCTTCTTGTTCTGTCGATTATTAGGATGAATGAGTTTGATGCAGGTCTCGATACTGTTAATTTCATA

Reverse complement sequence

TATGAAATTAACAGTATCGAGACCTGCATCAAACTCATTCATCCTAATAATCGACAGAACAAGAAGCTTCTATCGGTGCAATGTTTTTATTTTGTTTGTT[C/T]
TTATCTAATTGTTGTCATAAAGTTTGAATAAAGTTTGAAGATAACAAGTTCTCTCCTATACTGGATAACGTTTTTTTATAGGCTCTACATCATTTTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.70%	29.80%	0.34%	0.23%	NA
All Indica	2759	48.90%	50.10%	0.58%	0.40%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.00%	55.30%	0.34%	0.34%	NA
Indica II	465	78.90%	20.60%	0.22%	0.22%	NA
Indica III	913	33.70%	65.80%	0.00%	0.44%	NA
Indica Intermediate	786	52.50%	45.30%	1.65%	0.51%	NA
Temperate Japonica	767	99.90%	0.10%	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	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0314601404	G -> A	LOC_Os03g25550.1	upstream_gene_variant ; 1832.0bp to feature; MODIFIER	silent_mutation	Average:37.784; most accessible tissue: Callus, score: 54.35	N	N	N	N
vg0314601404	G -> A	LOC_Os03g25554.1	downstream_gene_variant ; 405.0bp to feature; MODIFIER	silent_mutation	Average:37.784; most accessible tissue: Callus, score: 54.35	N	N	N	N
vg0314601404	G -> A	LOC_Os03g25550-LOC_Os03g25554	intergenic_region ; MODIFIER	silent_mutation	Average:37.784; most accessible tissue: Callus, score: 54.35	N	N	N	N
vg0314601404	G -> DEL	N	N	silent_mutation	Average:37.784; most accessible tissue: Callus, score: 54.35	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314601404	7.57E-45	NA	mr1542	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
vg0314601404	2.61E-39	2.39E-62	mr1542	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
vg0314601404	NA	9.41E-08	mr1902	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
vg0314601404	5.90E-47	NA	mr1542_2	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
vg0314601404	5.54E-50	2.85E-69	mr1542_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
vg0314601404	NA	2.27E-06	mr1587_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