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Detailed information for vg0611621075:

Variant ID: vg0611621075 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11621075
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGCTCGCATCATGGATGAACAAGAAGATATCAAGATCAAGTCCTCCAAGTGCTGGAATCCGATTCGGCCACCTGTTACACTGCTAACTTCAAATGGCC[G/A]
CCGAATCTGCATACGACCTCCGTTTTCGGCCCGTGAGTACATGATGGAAAGCTCTCGGAGCCCTCTTTCCAAAGGATCCAGCCTCGTCATCAAATTCCAT

Reverse complement sequence

ATGGAATTTGATGACGAGGCTGGATCCTTTGGAAAGAGGGCTCCGAGAGCTTTCCATCATGTACTCACGGGCCGAAAACGGAGGTCGTATGCAGATTCGG[C/T]
GGCCATTTGAAGTTAGCAGTGTAACAGGTGGCCGAATCGGATTCCAGCACTTGGAGGACTTGATCTTGATATCTTCTTGTTCATCCATGATGCGAGCAAT

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	97.10%	2.90%	0.00%	0.00%	NA
All Indica	2759	95.20%	4.80%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	93.10%	6.90%	0.00%	0.00%	NA
Indica III	913	92.00%	8.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.70%	3.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0611621075	G -> A	LOC_Os06g20250.1	missense_variant ; p.Arg31Trp; MODERATE	nonsynonymous_codon ; R31W	Average:45.639; most accessible tissue: Zhenshan97 young leaf, score: 62.534	unknown	unknown	TOLERATED	0.17

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611621075	1.01E-09	7.89E-12	mr1695_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