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Detailed information for vg0825998077:

Variant ID: vg0825998077 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25998077
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGTACACGAAGTGCAGCAGAGCTCTGAACGTCGTCGGCTCGATGTCATGCAGCGTGACGCACGGCATGGTGGCCTCCGCCGTGGAGCCGAGGAGCTCC[A/G]
CCCTGAACACCGGCGAGCGCGCGGCGAGCACGGCCCGGTGCGCGTGGAACGTCTCACCGCCGACGGAGAAGGACACGTCCGAGCCGTCGGCGCTGCCCAC

Reverse complement sequence

GTGGGCAGCGCCGACGGCTCGGACGTGTCCTTCTCCGTCGGCGGTGAGACGTTCCACGCGCACCGGGCCGTGCTCGCCGCGCGCTCGCCGGTGTTCAGGG[T/C]
GGAGCTCCTCGGCTCCACGGCGGAGGCCACCATGCCGTGCGTCACGCTGCATGACATCGAGCCGACGACGTTCAGAGCTCTGCTGCACTTCGTGTACACG

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	58.90%	40.80%	0.25%	0.00%	NA
All Indica	2759	95.90%	3.80%	0.22%	0.00%	NA
All Japonica	1512	3.00%	97.00%	0.07%	0.00%	NA
Aus	269	13.80%	85.90%	0.37%	0.00%	NA
Indica I	595	98.70%	1.00%	0.34%	0.00%	NA
Indica II	465	96.30%	3.20%	0.43%	0.00%	NA
Indica III	913	95.40%	4.60%	0.00%	0.00%	NA
Indica Intermediate	786	94.30%	5.50%	0.25%	0.00%	NA
Temperate Japonica	767	2.30%	97.50%	0.13%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	46.70%	4.44%	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
vg0825998077	A -> G	LOC_Os08g41150.1	missense_variant ; p.Val208Ala; MODERATE	nonsynonymous_codon ; V208A	Average:71.485; most accessible tissue: Zhenshan97 panicle, score: 84.824	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825998077	NA	4.59E-21	mr1021	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
vg0825998077	NA	1.07E-26	mr1024	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
vg0825998077	NA	3.70E-15	mr1228	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
vg0825998077	NA	1.03E-15	mr1323	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
vg0825998077	NA	5.44E-39	mr1689_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