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Detailed information for vg0808162481:

Variant ID: vg0808162481 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8162481
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTGAGTGTCCCTGGGGTGGCGATGGAATAGAATCAAATCGAGCTAATAAACAGGTCGTGTTGTCTCAGAATGGGCGATATGGTACAAAACTTATTACCG[G/C]
ATGGATTCAGTCGGAGCCAAAGAACAGCGCGCAGAGCGACCTAGGGCTAGGAGTAGAGCTGCGTGGCGTACCTGCTCTCCACCCCACGTCGACGGCGCCG

Reverse complement sequence

CGGCGCCGTCGACGTGGGGTGGAGAGCAGGTACGCCACGCAGCTCTACTCCTAGCCCTAGGTCGCTCTGCGCGCTGTTCTTTGGCTCCGACTGAATCCAT[C/G]
CGGTAATAAGTTTTGTACCATATCGCCCATTCTGAGACAACACGACCTGTTTATTAGCTCGATTTGATTCTATTCCATCGCCACCCCAGGGACACTCACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.80%	7.70%	0.42%	2.05%	NA
All Indica	2759	95.70%	0.50%	0.43%	3.30%	NA
All Japonica	1512	86.00%	13.60%	0.20%	0.13%	NA
Aus	269	51.70%	46.10%	0.74%	1.49%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	82.60%	0.00%	1.72%	15.70%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	1.50%	0.51%	2.29%	NA
Temperate Japonica	767	95.70%	3.90%	0.39%	0.00%	NA
Tropical Japonica	504	80.80%	19.20%	0.00%	0.00%	NA
Japonica Intermediate	241	66.40%	32.80%	0.00%	0.83%	NA
VI/Aromatic	96	87.50%	10.40%	2.08%	0.00%	NA
Intermediate	90	87.80%	11.10%	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
vg0808162481	G -> C	LOC_Os08g13710.2	downstream_gene_variant ; 2829.0bp to feature; MODIFIER	silent_mutation	Average:48.89; most accessible tissue: Callus, score: 91.46	N	N	N	N
vg0808162481	G -> C	LOC_Os08g13699.1	intron_variant ; MODIFIER	silent_mutation	Average:48.89; most accessible tissue: Callus, score: 91.46	N	N	N	N
vg0808162481	G -> DEL	N	N	silent_mutation	Average:48.89; most accessible tissue: Callus, score: 91.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808162481	NA	2.02E-07	mr1345	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
vg0808162481	NA	2.19E-06	mr1427	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
vg0808162481	NA	6.54E-06	mr1759	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
vg0808162481	8.28E-06	7.15E-08	mr1876	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