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Detailed information for vg0806225198:

Variant ID: vg0806225198 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6225198
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGATTTATTGCACTATGAAATATCCCATCCAATCTTAGGTTGTGTTCTTATCTCAGGTTTTCCAACTCATCTCTCTTGTTTTCCACGCGCACGCTTTTT[A/G]
AAATGCTAAACGGTGTTTTTTTTTTGCAAAAAGTTTCTATACTAAAATTGCTTAACAAAATCACATTTATCCATTTTTGAAAAAAAAGCCAATACTTAAT

Reverse complement sequence

ATTAAGTATTGGCTTTTTTTTCAAAAATGGATAAATGTGATTTTGTTAAGCAATTTTAGTATAGAAACTTTTTGCAAAAAAAAAACACCGTTTAGCATTT[T/C]
AAAAAGCGTGCGCGTGGAAAACAAGAGAGATGAGTTGGAAAACCTGAGATAAGAACACAACCTAAGATTGGATGGGATATTTCATAGTGCAATAAATCTA

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	96.10%	3.70%	0.17%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	88.60%	11.00%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	98.70%	1.00%	0.26%	0.00%	NA
Tropical Japonica	504	73.40%	26.00%	0.60%	0.00%	NA
Japonica Intermediate	241	88.00%	11.60%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	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
vg0806225198	A -> G	LOC_Os08g10580.1	upstream_gene_variant ; 1074.0bp to feature; MODIFIER	silent_mutation	Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0806225198	A -> G	LOC_Os08g10570.1	downstream_gene_variant ; 1145.0bp to feature; MODIFIER	silent_mutation	Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0806225198	A -> G	LOC_Os08g10570.2	downstream_gene_variant ; 1145.0bp to feature; MODIFIER	silent_mutation	Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0806225198	A -> G	LOC_Os08g10570-LOC_Os08g10580	intergenic_region ; MODIFIER	silent_mutation	Average:53.929; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806225198	1.29E-06	7.97E-09	mr1039_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
vg0806225198	NA	9.13E-08	mr1632_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