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Detailed information for vg0724427457:

Variant ID: vg0724427457 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24427457
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGGGGAATATCTGAAGGGTTTGATGGAACGAGCAGCATATGCATATAGACAATCTGAGTTCAATGCTGCTATGCAAGAACTAAAGGTTAACAATTTGA[G/A]
GGCATGGGAGTGGCTAAGCAAGGTTCCAACCAAGCATTGGTGTAGATATATGTTTAGTTCTAGAGCAAAGACAGATCTTCTTCTTAACAACATAAGTGAA

Reverse complement sequence

TTCACTTATGTTGTTAAGAAGAAGATCTGTCTTTGCTCTAGAACTAAACATATATCTACACCAATGCTTGGTTGGAACCTTGCTTAGCCACTCCCATGCC[C/T]
TCAAATTGTTAACCTTTAGTTCTTGCATAGCAGCATTGAACTCAGATTGTCTATATGCATATGCTGCTCGTTCCATCAAACCCTTCAGATATTCCCCTCT

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	63.00%	36.40%	0.55%	0.00%	NA
All Indica	2759	95.20%	4.60%	0.22%	0.00%	NA
All Japonica	1512	1.10%	98.70%	0.20%	0.00%	NA
Aus	269	86.20%	9.30%	4.46%	0.00%	NA
Indica I	595	97.80%	2.00%	0.17%	0.00%	NA
Indica II	465	88.00%	12.00%	0.00%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	93.40%	6.10%	0.51%	0.00%	NA
Temperate Japonica	767	0.70%	99.30%	0.00%	0.00%	NA
Tropical Japonica	504	0.20%	99.40%	0.40%	0.00%	NA
Japonica Intermediate	241	4.60%	95.00%	0.41%	0.00%	NA
VI/Aromatic	96	65.60%	32.30%	2.08%	0.00%	NA
Intermediate	90	43.30%	53.30%	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
vg0724427457	G -> A	LOC_Os07g40760.1	missense_variant ; p.Arg856Lys; MODERATE	nonsynonymous_codon ; R856K	Average:12.281; most accessible tissue: Callus, score: 16.695	unknown	unknown	TOLERATED	0.29

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724427457	3.71E-06	4.16E-36	mr1181_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
vg0724427457	3.80E-07	1.51E-08	mr1181_2	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