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Detailed information for vg0825074071:

Variant ID: vg0825074071 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25074071
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CTTGCCTGTCCAGATGGACTAGCATCCGCGCCACTTGGAACTTCTGCATTCTTCGGGCATTTCTTGTAAGTATGGCCACGCAGATCACACTTGCTGCAGC[G/A]
TAAAGTCCTCCCACCTGCTTCTGATTTATCCATATCATTTCTGATGCGTCTAGTTTGGCGTCGACCCTTTTTCACCCTTAACTTAGATGGATCTAGAATA

Reverse complement sequence

TATTCTAGATCCATCTAAGTTAAGGGTGAAAAAGGGTCGACGCCAAACTAGACGCATCAGAAATGATATGGATAAATCAGAAGCAGGTGGGAGGACTTTA[C/T]
GCTGCAGCAAGTGTGATCTGCGTGGCCATACTTACAAGAAATGCCCGAAGAATGCAGAAGTTCCAAGTGGCGCGGATGCTAGTCCATCTGGACAGGCAAG

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	82.30%	17.60%	0.15%	0.00%	NA
All Indica	2759	70.20%	29.60%	0.25%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	67.60%	31.80%	0.67%	0.00%	NA
Indica II	465	78.70%	21.10%	0.22%	0.00%	NA
Indica III	913	59.00%	41.00%	0.00%	0.00%	NA
Indica Intermediate	786	80.00%	19.70%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0825074071	G -> A	LOC_Os08g39620.1	missense_variant ; p.Arg817Cys; MODERATE	nonsynonymous_codon ; R817C	Average:21.242; most accessible tissue: Minghui63 flag leaf, score: 38.136	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825074071	1.24E-06	NA	mr1874	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
vg0825074071	1.58E-06	1.27E-11	mr1874	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
vg0825074071	2.31E-07	NA	mr1874_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
vg0825074071	4.67E-07	5.27E-13	mr1874_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