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Detailed information for vg0203404863:

Variant ID: vg0203404863 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3404863
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TATTCCTCCAAATCTTGGTAGTCCGCCCATCTCTTACCCTCCAAATCAGTCCTCTCTTTAGCAATTCCAGCCCATGTTCGATTCCTTTCCAAGTTGGTGA[A/G]
GTATTGGACGGGAAAGCTGTATCAATAAGGGAGCCATTGGGGTAGTACTTTGCTTTTAGCAACCTAGCGCACAAGCTATTTGGCTCCGCGATCAACCTCC

Reverse complement sequence

GGAGGTTGATCGCGGAGCCAAATAGCTTGTGCGCTAGGTTGCTAAAAGCAAAGTACTACCCCAATGGCTCCCTTATTGATACAGCTTTCCCGTCCAATAC[T/C]
TCACCAACTTGGAAAGGAATCGAACATGGGCTGGAATTGCTAAAGAGAGGACTGATTTGGAGGGTAAGAGATGGGCGGACTACCAAGATTTGGAGGAATA

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	22.50%	7.20%	1.12%	69.19%	NA
All Indica	2759	7.10%	0.40%	1.38%	91.05%	NA
All Japonica	1512	39.70%	21.00%	0.79%	38.56%	NA
Aus	269	85.50%	0.00%	0.00%	14.50%	NA
Indica I	595	7.40%	0.20%	3.03%	89.41%	NA
Indica II	465	1.70%	0.60%	1.08%	96.56%	NA
Indica III	913	8.30%	0.20%	0.44%	91.02%	NA
Indica Intermediate	786	8.80%	0.80%	1.40%	89.06%	NA
Temperate Japonica	767	36.40%	33.20%	1.04%	29.34%	NA
Tropical Japonica	504	52.80%	1.40%	0.60%	45.24%	NA
Japonica Intermediate	241	22.80%	22.80%	0.41%	53.94%	NA
VI/Aromatic	96	7.30%	0.00%	1.04%	91.67%	NA
Intermediate	90	34.40%	10.00%	2.22%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203404863	A -> G	LOC_Os02g06750.1	synonymous_variant ; p.Thr227Thr; LOW	synonymous_codon	Average:9.97; most accessible tissue: Callus, score: 28.796	N	N	N	N
vg0203404863	A -> DEL	LOC_Os02g06750.1	N	frameshift_variant	Average:9.97; most accessible tissue: Callus, score: 28.796	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203404863	7.43E-06	NA	mr1897	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
vg0203404863	NA	2.51E-08	mr1010_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
vg0203404863	NA	3.76E-09	mr1709_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