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Detailed information for vg0806410047:

Variant ID: vg0806410047 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6410047
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTAAACAAAGGTTAGAGAAGGGTTTTTGTTTGTTGTGGCTCGGTTTGGTAGTTCTCCTCCGTTGGCAGATTTGCATTGTTTCGGTTTTTTTGTTGTTTC[G/A,T]
GGGGTCTAAATGATGTTTTCTACGAAAGTGTATAACTAGGAAGTTGTAGAAAATTCATAGACCTATCTTCTGACCAGAGGGCGCAATTTTATCTTTAGTT

Reverse complement sequence

AACTAAAGATAAAATTGCGCCCTCTGGTCAGAAGATAGGTCTATGAATTTTCTACAACTTCCTAGTTATACACTTTCGTAGAAAACATCATTTAGACCCC[C/T,A]
GAAACAACAAAAAAACCGAAACAATGCAAATCTGCCAACGGAGGAGAACTACCAAACCGAGCCACAACAAACAAAAACCCTTCTCTAACCTTTGTTTACC

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	65.50%	24.50%	5.67%	4.19%	T: 0.06%
All Indica	2759	45.10%	40.80%	8.37%	5.65%	T: 0.11%
All Japonica	1512	97.80%	0.70%	0.46%	0.99%	NA
Aus	269	82.90%	0.40%	8.92%	7.81%	NA
Indica I	595	48.90%	43.40%	6.89%	0.84%	NA
Indica II	465	47.10%	37.00%	3.87%	12.04%	NA
Indica III	913	32.50%	51.00%	11.17%	5.15%	T: 0.11%
Indica Intermediate	786	55.60%	29.10%	8.91%	6.11%	T: 0.25%
Temperate Japonica	767	98.70%	0.80%	0.52%	0.00%	NA
Tropical Japonica	504	96.00%	0.80%	0.40%	2.78%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	94.80%	1.00%	2.08%	2.08%	NA
Intermediate	90	66.70%	24.40%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806410047	G -> T	LOC_Os08g10880.1	downstream_gene_variant ; 1828.0bp to feature; MODIFIER	silent_mutation	Average:41.757; most accessible tissue: Callus, score: 65.394	N	N	N	N
vg0806410047	G -> T	LOC_Os08g10870-LOC_Os08g10880	intergenic_region ; MODIFIER	silent_mutation	Average:41.757; most accessible tissue: Callus, score: 65.394	N	N	N	N
vg0806410047	G -> A	LOC_Os08g10880.1	downstream_gene_variant ; 1828.0bp to feature; MODIFIER	silent_mutation	Average:41.757; most accessible tissue: Callus, score: 65.394	N	N	N	N
vg0806410047	G -> A	LOC_Os08g10870-LOC_Os08g10880	intergenic_region ; MODIFIER	silent_mutation	Average:41.757; most accessible tissue: Callus, score: 65.394	N	N	N	N
vg0806410047	G -> DEL	N	N	silent_mutation	Average:41.757; most accessible tissue: Callus, score: 65.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806410047	2.72E-06	NA	mr1728	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