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Detailed information for vg0808625370:

Variant ID: vg0808625370 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8625370
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCCGCCTCGTCCGCCGCCGACTGGTGTTTCCGCCTGCACGGCTGGCCTTTATGCCGCCGTTGTTGGGCGTCTACGTCTTCACCGACCGGCCGTCTCGTC[C/T]
GCTGCCGACTGGTGTTTCTGCCTGCACTGCTGGCCTATTATGCCGCCGTTGTCGGACGTGTACATCTTCACCGACTGGCCGCCTCGTCCGCCGCCGATTG

Reverse complement sequence

CAATCGGCGGCGGACGAGGCGGCCAGTCGGTGAAGATGTACACGTCCGACAACGGCGGCATAATAGGCCAGCAGTGCAGGCAGAAACACCAGTCGGCAGC[G/A]
GACGAGACGGCCGGTCGGTGAAGACGTAGACGCCCAACAACGGCGGCATAAAGGCCAGCCGTGCAGGCGGAAACACCAGTCGGCGGCGGACGAGGCGGCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.00%	12.30%	0.72%	0.00%	NA
All Indica	2759	78.10%	20.60%	1.23%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	81.70%	16.80%	1.51%	0.00%	NA
Indica II	465	93.30%	6.20%	0.43%	0.00%	NA
Indica III	913	67.50%	31.70%	0.88%	0.00%	NA
Indica Intermediate	786	78.90%	19.20%	1.91%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0808625370	C -> T	LOC_Os08g14370.1	downstream_gene_variant ; 1011.0bp to feature; MODIFIER	silent_mutation	Average:56.73; most accessible tissue: Zhenshan97 flag leaf, score: 87.087	N	N	N	N
vg0808625370	C -> T	LOC_Os08g14380.1	downstream_gene_variant ; 279.0bp to feature; MODIFIER	silent_mutation	Average:56.73; most accessible tissue: Zhenshan97 flag leaf, score: 87.087	N	N	N	N
vg0808625370	C -> T	LOC_Os08g14370-LOC_Os08g14380	intergenic_region ; MODIFIER	silent_mutation	Average:56.73; most accessible tissue: Zhenshan97 flag leaf, score: 87.087	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808625370	9.16E-06	NA	mr1740	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
vg0808625370	NA	7.51E-06	mr1740	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