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Detailed information for vg0500226250:

Variant ID: vg0500226250 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 226250
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

CATAGGATTGTTGTTTTGTTTTGATAGGATAAGATGGGCTACATAATTTTAGGTATCGCTAGGATTTAATTTACACTGTAGACAAAACATAAGGCCTTTT[G/T]
TGTCTAATAGAAGAAAGAAAGATGGAGAGCATTTGCCCCTGTTGGAACAATTAATGTGCTGCAGGCAATAACAATCCAGTTGGTTGGCCATTACGATTCC

Reverse complement sequence

GGAATCGTAATGGCCAACCAACTGGATTGTTATTGCCTGCAGCACATTAATTGTTCCAACAGGGGCAAATGCTCTCCATCTTTCTTTCTTCTATTAGACA[C/A]
AAAAGGCCTTATGTTTTGTCTACAGTGTAAATTAAATCCTAGCGATACCTAAAATTATGTAGCCCATCTTATCCTATCAAAACAAAACAACAATCCTATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.80%	5.20%	0.02%	0.00%	NA
All Indica	2759	91.30%	8.70%	0.04%	0.00%	NA
All Japonica	1512	99.80%	0.20%	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	88.40%	11.60%	0.00%	0.00%	NA
Indica III	913	88.70%	11.30%	0.00%	0.00%	NA
Indica Intermediate	786	89.60%	10.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0500226250	G -> T	LOC_Os05g01360.1	3_prime_UTR_variant ; 364.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500226250	G -> T	LOC_Os05g01370.1	upstream_gene_variant ; 758.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500226250	G -> T	LOC_Os05g01380.1	upstream_gene_variant ; 4534.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0500226250	3.71E-06	NA	mr1146_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