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Detailed information for vg0422260209:

Variant ID: vg0422260209 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 22260209
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: 350. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCTGATGAAATTTTGCAGTTGTTATTGAGGAAATTCAAGAGGATGACAAGCCTGCTGCTGGTGGAGCACAAAAGGGATCAAACAAGAAGCAAACCAGC[G/A]
AAAATGGTGATGATTCTAAACTGCAGCTTGTTGTTAGGACTCCACCTGCTGAATCTTTGGAAAGCGAAGATGAAGATGGCTTTCCTGTATCATTTTCTGA

Reverse complement sequence

TCAGAAAATGATACAGGAAAGCCATCTTCATCTTCGCTTTCCAAAGATTCAGCAGGTGGAGTCCTAACAACAAGCTGCAGTTTAGAATCATCACCATTTT[C/T]
GCTGGTTTGCTTCTTGTTTGATCCCTTTTGTGCTCCACCAGCAGCAGGCTTGTCATCCTCTTGAATTTCCTCAATAACAACTGCAAAATTTCATCAGAAG

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	97.30%	2.50%	0.15%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	92.10%	7.50%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	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	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	98.40%	1.40%	0.13%	0.00%	NA
Tropical Japonica	504	81.00%	18.70%	0.40%	0.00%	NA
Japonica Intermediate	241	95.40%	3.30%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0422260209	G -> A	LOC_Os04g36890.1	missense_variant ; p.Glu210Lys; MODERATE	nonsynonymous_codon ; E210K	Average:44.531; most accessible tissue: Callus, score: 79.393	benign	0.278	TOLERATED	0.19
vg0422260209	G -> A	LOC_Os04g36890.2	missense_variant ; p.Glu39Lys; MODERATE	nonsynonymous_codon ; E39K	Average:44.531; most accessible tissue: Callus, score: 79.393	benign	0.278	TOLERATED	0.33

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0422260209	1.68E-06	1.68E-06	mr1085	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
vg0422260209	NA	1.08E-06	mr1104	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
vg0422260209	7.69E-08	2.64E-09	mr1155	Jap_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
vg0422260209	NA	2.40E-07	mr1213	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
vg0422260209	NA	4.83E-09	mr1248	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
vg0422260209	4.70E-06	4.70E-06	mr1264	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
vg0422260209	NA	6.03E-06	mr1277	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
vg0422260209	NA	6.45E-12	mr1410	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
vg0422260209	NA	6.03E-07	mr1411	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
vg0422260209	NA	8.28E-07	mr1437	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
vg0422260209	NA	5.51E-07	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
vg0422260209	NA	3.52E-08	mr1746	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
vg0422260209	NA	3.32E-06	mr1155_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