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Detailed information for vg0401249456:

Variant ID: vg0401249456 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1249456
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, G: 0.44, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGGATGCATGGATCTAATCATCTAATTACAAATTTGTGTATTGCAAAATGTGATATGGAATGATTTTTTCAATGATAATATATATAGTTGTGAAAAGT[T/G]
ACAACGTTTCTTTATGATTAAATGGATTGCCTCTTATATGCAAAAGCTTACTAATAGCCAATAACAGAAACATAGCAACCGATCGACACAAACATTATGA

Reverse complement sequence

TCATAATGTTTGTGTCGATCGGTTGCTATGTTTCTGTTATTGGCTATTAGTAAGCTTTTGCATATAAGAGGCAATCCATTTAATCATAAAGAAACGTTGT[A/C]
ACTTTTCACAACTATATATATTATCATTGAAAAAATCATTCCATATCACATTTTGCAATACACAAATTTGTAATTAGATGATTAGATCCATGCATCCCGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.90%	30.90%	0.21%	0.00%	NA
All Indica	2759	81.80%	18.00%	0.18%	0.00%	NA
All Japonica	1512	39.40%	60.40%	0.13%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	73.10%	26.70%	0.22%	0.00%	NA
Indica III	913	73.80%	26.10%	0.11%	0.00%	NA
Indica Intermediate	786	84.40%	15.30%	0.38%	0.00%	NA
Temperate Japonica	767	55.70%	44.10%	0.26%	0.00%	NA
Tropical Japonica	504	18.30%	81.70%	0.00%	0.00%	NA
Japonica Intermediate	241	32.00%	68.00%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	64.40%	32.20%	3.33%	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
vg0401249456	T -> G	LOC_Os04g03040.1	upstream_gene_variant ; 3529.0bp to feature; MODIFIER	silent_mutation	Average:38.353; most accessible tissue: Callus, score: 69.665	N	N	N	N
vg0401249456	T -> G	LOC_Os04g03050.1	intron_variant ; MODIFIER	silent_mutation	Average:38.353; most accessible tissue: Callus, score: 69.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401249456	NA	5.54E-09	mr1182	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
vg0401249456	NA	3.65E-08	mr1282	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
vg0401249456	2.45E-06	2.45E-06	mr1473	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
vg0401249456	NA	3.31E-06	mr1648	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
vg0401249456	9.59E-06	1.43E-08	mr1650	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
vg0401249456	NA	2.26E-07	mr1658	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
vg0401249456	NA	3.25E-07	mr1182_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
vg0401249456	NA	2.27E-06	mr1195_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
vg0401249456	NA	1.02E-06	mr1282_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
vg0401249456	NA	8.33E-06	mr1296_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
vg0401249456	NA	3.26E-07	mr1474_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
vg0401249456	NA	6.27E-06	mr1539_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
vg0401249456	NA	4.03E-07	mr1566_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
vg0401249456	NA	9.22E-06	mr1566_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