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Detailed information for vg0313617458:

Variant ID: vg0313617458 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13617458
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: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCAATAAGTCGCTCGTAAAACATATGGTATTTGAAAAAGGCAAGCGAATACGTGTGGTCGAGAAGGACGCTGAGGCGGTTACTCAGGAATCAGACTCA[G/A]
CATATCCAGACTCCGATCTCCATGTCTCGCACATCTTCGGAGGTTCCACGACATACTCCTCAGAGCGAGAATACAAGAAGGTGAAACGTGAAGTTTGTTC

Reverse complement sequence

GAACAAACTTCACGTTTCACCTTCTTGTATTCTCGCTCTGAGGAGTATGTCGTGGAACCTCCGAAGATGTGCGAGACATGGAGATCGGAGTCTGGATATG[C/T]
TGAGTCTGATTCCTGAGTAACCGCCTCAGCGTCCTTCTCGACCACACGTATTCGCTTGCCTTTTTCAAATACCATATGTTTTACGAGCGACTTATTGAAG

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	84.40%	11.90%	1.23%	2.50%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	57.90%	32.50%	2.84%	6.81%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.60%	6.90%	0.39%	0.13%	NA
Tropical Japonica	504	17.30%	58.70%	6.55%	17.46%	NA
Japonica Intermediate	241	32.40%	58.90%	2.90%	5.81%	NA
VI/Aromatic	96	19.80%	54.20%	13.54%	12.50%	NA
Intermediate	90	76.70%	18.90%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0313617458	G -> A	LOC_Os03g23990.1	missense_variant ; p.Ala563Thr; MODERATE	nonsynonymous_codon ; A563T	Average:47.96; most accessible tissue: Minghui63 flag leaf, score: 73.334	possibly damaging	1.571	DELETERIOUS	0.05
vg0313617458	G -> DEL	LOC_Os03g23990.1	N	frameshift_variant	Average:47.96; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313617458	NA	2.88E-14	mr1084	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
vg0313617458	NA	1.46E-12	mr1205	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
vg0313617458	NA	3.15E-07	mr1206	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
vg0313617458	NA	5.79E-07	mr1319	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
vg0313617458	NA	2.10E-09	mr1322	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
vg0313617458	NA	3.44E-17	mr1330	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
vg0313617458	NA	7.22E-07	mr1330	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
vg0313617458	NA	2.63E-11	mr1332	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
vg0313617458	NA	1.71E-11	mr1336	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
vg0313617458	NA	1.35E-06	mr1338	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
vg0313617458	NA	9.37E-13	mr1454	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
vg0313617458	NA	8.46E-13	mr1521	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
vg0313617458	4.06E-06	3.01E-15	mr1579	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
vg0313617458	NA	3.91E-06	mr1579	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
vg0313617458	NA	6.81E-20	mr1580	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
vg0313617458	NA	9.90E-17	mr1701	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
vg0313617458	NA	8.01E-11	mr1775	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
vg0313617458	NA	1.89E-07	mr1779	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
vg0313617458	NA	3.82E-21	mr1825	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