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Detailed information for vg0805645208:

Variant ID: vg0805645208 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5645208
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATATTTGGACACTTATTATAAATATTAAACATAGACTATTAATAAAACATATCTATAATCTTGGACTAATTCGCGAGACGAATCTATTGAGTCTAATTA[A/G]
TCCATGATTAGCCTATGTGATGCTATAGTAAACATTATCTAATTATGAATTAATTAGGCTTAAAAAATTTGTCTCACGAATTAGCTTTCATTTATGTAAT

Reverse complement sequence

ATTACATAAATGAAAGCTAATTCGTGAGACAAATTTTTTAAGCCTAATTAATTCATAATTAGATAATGTTTACTATAGCATCACATAGGCTAATCATGGA[T/C]
TAATTAGACTCAATAGATTCGTCTCGCGAATTAGTCCAAGATTATAGATATGTTTTATTAATAGTCTATGTTTAATATTTATAATAAGTGTCCAAATATC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	22.30%	0.17%	0.04%	NA
All Indica	2759	71.30%	28.30%	0.25%	0.07%	NA
All Japonica	1512	94.10%	5.90%	0.00%	0.00%	NA
Aus	269	46.10%	53.90%	0.00%	0.00%	NA
Indica I	595	93.80%	5.90%	0.17%	0.17%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	43.70%	55.80%	0.44%	0.11%	NA
Indica Intermediate	786	75.10%	24.70%	0.25%	0.00%	NA
Temperate Japonica	767	98.60%	1.40%	0.00%	0.00%	NA
Tropical Japonica	504	91.70%	8.30%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	1.11%	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
vg0805645208	A -> G	LOC_Os08g09760.1	downstream_gene_variant ; 1934.0bp to feature; MODIFIER	silent_mutation	Average:44.146; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645208	A -> G	LOC_Os08g09770.1	downstream_gene_variant ; 469.0bp to feature; MODIFIER	silent_mutation	Average:44.146; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645208	A -> G	LOC_Os08g09760.2	downstream_gene_variant ; 1943.0bp to feature; MODIFIER	silent_mutation	Average:44.146; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645208	A -> G	LOC_Os08g09760-LOC_Os08g09770	intergenic_region ; MODIFIER	silent_mutation	Average:44.146; most accessible tissue: Callus, score: 69.292	N	N	N	N
vg0805645208	A -> DEL	N	N	silent_mutation	Average:44.146; most accessible tissue: Callus, score: 69.292	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805645208	1.02E-06	1.65E-08	mr1167_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
vg0805645208	NA	1.37E-06	mr1950_2	Ind_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