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Detailed information for vg0208637781:

Variant ID: vg0208637781 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8637781
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, T: 0.12, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

CGGTCATGGACATGCTCGGTGATATCTCATGAGGGGTAGTTTGTGAAAACTGGGAATGAACTGTGTGTAGGTTGATTAATATAGCTATGTGGTCCTGTGT[G/T]
GATGGATAGTTGGTAACACCCGTTATTTATAATTGTTGTTTTAAATCTCTGTTTATAAATTGTTTATAACTGCAAATTGCAAATTGTTGTGTTATGCAAA

Reverse complement sequence

TTTGCATAACACAACAATTTGCAATTTGCAGTTATAAACAATTTATAAACAGAGATTTAAAACAACAATTATAAATAACGGGTGTTACCAACTATCCATC[C/A]
ACACAGGACCACATAGCTATATTAATCAACCTACACACAGTTCATTCCCAGTTTTCACAAACTACCCCTCATGAGATATCACCGAGCATGTCCATGACCG

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	29.90%	17.30%	4.85%	48.01%	NA
All Indica	2759	18.90%	20.50%	7.50%	53.10%	NA
All Japonica	1512	56.20%	1.00%	0.60%	42.26%	NA
Aus	269	4.50%	70.30%	1.86%	23.42%	NA
Indica I	595	21.30%	7.10%	8.40%	63.19%	NA
Indica II	465	8.00%	30.80%	8.60%	52.69%	NA
Indica III	913	21.10%	25.00%	7.01%	46.88%	NA
Indica Intermediate	786	20.90%	19.50%	6.74%	52.93%	NA
Temperate Japonica	767	81.20%	0.30%	0.13%	18.38%	NA
Tropical Japonica	504	28.80%	1.60%	1.19%	68.45%	NA
Japonica Intermediate	241	33.60%	2.10%	0.83%	63.49%	NA
VI/Aromatic	96	3.10%	24.00%	1.04%	71.88%	NA
Intermediate	90	30.00%	25.60%	7.78%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208637781	G -> T	LOC_Os02g15430.1	downstream_gene_variant ; 2545.0bp to feature; MODIFIER	silent_mutation	Average:13.032; most accessible tissue: Callus, score: 64.229	N	N	N	N
vg0208637781	G -> T	LOC_Os02g15420-LOC_Os02g15430	intergenic_region ; MODIFIER	silent_mutation	Average:13.032; most accessible tissue: Callus, score: 64.229	N	N	N	N
vg0208637781	G -> DEL	N	N	silent_mutation	Average:13.032; most accessible tissue: Callus, score: 64.229	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208637781	3.08E-06	6.93E-06	mr1748_2	Jap_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
vg0208637781	NA	2.22E-06	mr1944_2	Jap_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