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Detailed information for vg0608047686:

Variant ID: vg0608047686 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8047686
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:

GGGAAAGTTAACTTAGGATCACAAGGAACTTTTAATTCTATGTCTGCATCACAAATGGATTACCCCACAGTTCCTCCTTATGTGTCTTCTTCCTTTGGAG[G/A]
TGGTCCACAGTATCTTGACAAAGGGAAAGACTTGACTTCAGGCAATACTGGCAGTGAACTAAATTCTTCTAAAGCTGGAGCTCAGCTGGGGATCATGCAT

Reverse complement sequence

ATGCATGATCCCCAGCTGAGCTCCAGCTTTAGAAGAATTTAGTTCACTGCCAGTATTGCCTGAAGTCAAGTCTTTCCCTTTGTCAAGATACTGTGGACCA[C/T]
CTCCAAAGGAAGAAGACACATAAGGAGGAACTGTGGGGTAATCCATTTGTGATGCAGACATAGAATTAAAAGTTCCTTGTGATCCTAAGTTAACTTTCCC

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	94.90%	3.90%	1.27%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	84.50%	11.70%	3.77%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	78.60%	16.90%	4.43%	0.00%	NA
Tropical Japonica	504	95.00%	3.40%	1.59%	0.00%	NA
Japonica Intermediate	241	81.30%	12.40%	6.22%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0608047686	G -> A	LOC_Os06g14406.1	missense_variant ; p.Gly398Asp; MODERATE	nonsynonymous_codon ; G398D	Average:57.0; most accessible tissue: Callus, score: 79.287	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608047686	NA	1.83E-06	mr1002	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
vg0608047686	NA	2.37E-08	mr1794_2	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