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Detailed information for vg1011809445:

Variant ID: vg1011809445 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11809445
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: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CAAATGTCTGGTGGAATTATTCATGAACAGTTCAACAATTTGAAGTGTCTTGATCATTTCATATACTGCACAACTGGTTACTTCACCTGGAGCAAACTCA[G/A]
CTATATCGACCTTCAGCTGCAAAACTTCATCTTCTAATTTTCCTATTTCTGAGGAGGTATCCATGATTTTTCTGAATGAAGCCTGCAAATTTGAGCCTAA

Reverse complement sequence

TTAGGCTCAAATTTGCAGGCTTCATTCAGAAAAATCATGGATACCTCCTCAGAAATAGGAAAATTAGAAGATGAAGTTTTGCAGCTGAAGGTCGATATAG[C/T]
TGAGTTTGCTCCAGGTGAAGTAACCAGTTGTGCAGTATATGAAATGATCAAGACACTTCAAATTGTTGAACTGTTCATGAATAATTCCACCAGACATTTG

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	93.50%	6.50%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	79.90%	20.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	61.30%	38.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1011809445	G -> A	LOC_Os10g22730.1	missense_variant ; p.Ala172Val; MODERATE	nonsynonymous_codon ; A172V	Average:30.491; most accessible tissue: Callus, score: 73.074	unknown	unknown	TOLERATED	0.29
vg1011809445	G -> A	LOC_Os10g22730.2	missense_variant ; p.Ala172Val; MODERATE	nonsynonymous_codon ; A172V	Average:30.491; most accessible tissue: Callus, score: 73.074	unknown	unknown	TOLERATED	0.29
vg1011809445	G -> A	LOC_Os10g22730.3	missense_variant ; p.Ala172Val; MODERATE	nonsynonymous_codon ; A172V	Average:30.491; most accessible tissue: Callus, score: 73.074	unknown	unknown	TOLERATED	0.29
vg1011809445	G -> A	LOC_Os10g22730.4	missense_variant ; p.Ala172Val; MODERATE	nonsynonymous_codon ; A172V	Average:30.491; most accessible tissue: Callus, score: 73.074	unknown	unknown	TOLERATED	0.29

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011809445	1.25E-06	NA	mr1920	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