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Detailed information for vg0814594496:

Variant ID: vg0814594496 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14594496
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAGGTGTGTGGGCAGTCTGACCGGCTAGTAGGGCCAGTCTGACCGCAGGTATATGGGCGGTCAGACCGTCAGGGTCCGAGTCCGAGTCTGTTTTCGTC[G/T]
GGTCTCGAGTTTCCTTGCTCGGGAAGGCATGTTTCGTGTTTCCTTTGGTTTCTATCCCGAGTTGGGCATGGAGAAGGACCTGTAGAGGGCAAGACCAATC

Reverse complement sequence

GATTGGTCTTGCCCTCTACAGGTCCTTCTCCATGCCCAACTCGGGATAGAAACCAAAGGAAACACGAAACATGCCTTCCCGAGCAAGGAAACTCGAGACC[C/A]
GACGAAAACAGACTCGGACTCGGACCCTGACGGTCTGACCGCCCATATACCTGCGGTCAGACTGGCCCTACTAGCCGGTCAGACTGCCCACACACCTGTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.70%	12.50%	0.17%	0.68%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	59.50%	38.00%	0.53%	1.98%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	47.60%	48.90%	0.91%	2.61%	NA
Tropical Japonica	504	72.00%	26.60%	0.20%	1.19%	NA
Japonica Intermediate	241	71.40%	27.00%	0.00%	1.66%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	11.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814594496	G -> T	LOC_Os08g24170.1	upstream_gene_variant ; 803.0bp to feature; MODIFIER	silent_mutation	Average:68.588; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0814594496	G -> T	LOC_Os08g24170-LOC_Os08g24182	intergenic_region ; MODIFIER	silent_mutation	Average:68.588; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N
vg0814594496	G -> DEL	N	N	silent_mutation	Average:68.588; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814594496	1.70E-07	4.63E-10	mr1708	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
vg0814594496	4.69E-06	1.60E-07	mr1708	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
vg0814594496	4.73E-06	4.73E-06	mr1806	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