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Detailed information for vg0100356236:

Variant ID: vg0100356236 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 356236
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTTTATAAAAAAACATTGATGTAATGTCTTGTTTAATTAGGAAAGCATCCATAATGTAGAACACTATTGAACAAGCTTCTCCATGGTGCAGTGCTT[G/A]
TTTATTATGCTCCCTATGGTATGACATTTATTATTCTCTCTTTTTTCCTGCCAAACTTTGGCTCGATAGTTTCACTTGAAGATTCAGATTTATGGAGAAC

Reverse complement sequence

GTTCTCCATAAATCTGAATCTTCAAGTGAAACTATCGAGCCAAAGTTTGGCAGGAAAAAAGAGAGAATAATAAATGTCATACCATAGGGAGCATAATAAA[C/T]
AAGCACTGCACCATGGAGAAGCTTGTTCAATAGTGTTCTACATTATGGATGCTTTCCTAATTAAACAAGACATTACATCAATGTTTTTTTATAAAAAAAA

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	95.20%	4.80%	0.00%	0.00%	NA
All Indica	2759	98.70%	1.30%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	39.00%	61.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.90%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0100356236	G -> A	LOC_Os01g01689.1	missense_variant ; p.Val1506Ile; MODERATE	nonsynonymous_codon ; V1506I	Average:34.493; most accessible tissue: Callus, score: 71.082	unknown	unknown	TOLERATED	0.37
vg0100356236	G -> A	LOC_Os01g01689.3	missense_variant ; p.Val1506Ile; MODERATE	nonsynonymous_codon ; V1506I	Average:34.493; most accessible tissue: Callus, score: 71.082	unknown	unknown	TOLERATED	0.41

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100356236	NA	4.00E-08	mr1415	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
vg0100356236	NA	4.00E-08	mr1567	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
vg0100356236	NA	1.72E-08	mr1570	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
vg0100356236	NA	9.51E-17	mr1113_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
vg0100356236	5.73E-06	4.32E-18	mr1117_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
vg0100356236	1.95E-06	3.61E-18	mr1119_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
vg0100356236	NA	1.10E-22	mr1120_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
vg0100356236	NA	9.36E-09	mr1166_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
vg0100356236	NA	1.71E-10	mr1567_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
vg0100356236	8.59E-07	9.26E-22	mr1961_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