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Detailed information for vg0509824684:

Variant ID: vg0509824684 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 9824684
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TGATTCAGGAGCTACGCATTCCTTTATATCAAGAGATTTTGTGGCAAAACACCAAATAAGGATAGAAGATCTTAGCAACCCTATGATAATATCAACCCCG[G/A]
GAAGCCAGCTACCGACTAAGCTCTTCAGCCCATCAGTAACCATAGAGATCCAAGGAGTCACTTTTCTGGCTAATCTCATCCTTCTGAGCTCTAAGAACCC

Reverse complement sequence

GGGTTCTTAGAGCTCAGAAGGATGAGATTAGCCAGAAAAGTGACTCCTTGGATCTCTATGGTTACTGATGGGCTGAAGAGCTTAGTCGGTAGCTGGCTTC[C/T]
CGGGGTTGATATTATCATAGGGTTGCTAAGATCTTCTATCCTTATTTGGTGTTTTGCCACAAAATCTCTTGATATAAAGGAATGCGTAGCTCCTGAATCA

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	91.90%	8.00%	0.15%	0.00%	NA
All Indica	2759	92.60%	7.20%	0.22%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	37.90%	61.70%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	82.70%	16.60%	0.66%	0.00%	NA
Indica Intermediate	786	94.30%	5.70%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0509824684	G -> A	LOC_Os05g17150.1	missense_variant ; p.Gly470Arg; MODERATE	nonsynonymous_codon ; G470R	Average:59.666; most accessible tissue: Minghui63 flag leaf, score: 75.341	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0509824684	8.10E-06	NA	mr1131_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
vg0509824684	5.12E-07	NA	mr1316_2	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
vg0509824684	1.70E-06	NA	mr1386_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
vg0509824684	6.17E-06	NA	mr1541_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
vg0509824684	5.50E-06	NA	mr1743_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
vg0509824684	NA	7.20E-08	mr1762_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
vg0509824684	NA	8.50E-10	mr1818_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
vg0509824684	4.32E-06	NA	mr1938_2	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