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Detailed information for vg0818493992:

Variant ID: vg0818493992 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18493992
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATATTTCTTTTTTTTAATTTCAAATTTTCTGTAAATTGTATTTGTAAATTAATAATATTCCTATATTATTTATTTTTATTTCTGAATTTTTATTATTT[C/G]
TAATTGTATTTCTATATGGACTCTAAACTCATCTTTCAATATTCTTTAATTTTTAATTTTGAATTTCAGTTACTTCTAAACTGTATTCCTATACTTGTAT

Reverse complement sequence

ATACAAGTATAGGAATACAGTTTAGAAGTAACTGAAATTCAAAATTAAAAATTAAAGAATATTGAAAGATGAGTTTAGAGTCCATATAGAAATACAATTA[G/C]
AAATAATAAAAATTCAGAAATAAAAATAAATAATATAGGAATATTATTAATTTACAAATACAATTTACAGAAAATTTGAAATTAAAAAAAAGAAATATGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.40%	11.50%	0.13%	0.00%	NA
All Indica	2759	80.40%	19.40%	0.22%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.50%	3.50%	0.00%	0.00%	NA
Indica II	465	94.20%	5.80%	0.00%	0.00%	NA
Indica III	913	66.50%	33.40%	0.11%	0.00%	NA
Indica Intermediate	786	76.10%	23.30%	0.64%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	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
vg0818493992	C -> G	LOC_Os08g30080.1	upstream_gene_variant ; 728.0bp to feature; MODIFIER	silent_mutation	Average:16.426; most accessible tissue: Callus, score: 31.044	N	N	N	N
vg0818493992	C -> G	LOC_Os08g30090.1	downstream_gene_variant ; 2977.0bp to feature; MODIFIER	silent_mutation	Average:16.426; most accessible tissue: Callus, score: 31.044	N	N	N	N
vg0818493992	C -> G	LOC_Os08g30080-LOC_Os08g30090	intergenic_region ; MODIFIER	silent_mutation	Average:16.426; most accessible tissue: Callus, score: 31.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818493992	1.75E-06	2.90E-08	mr1793_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