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Detailed information for vg0809186402:

Variant ID: vg0809186402 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9186402
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTGCTGCTATTGAGGACTTGCTGGGAGTTTAGTGGGGCTCCGCCTCCACCCTCCCTCGTCATAGGAGTTTTATTTTTCTTTAAGTAGTTTTCCGTAAC[A/T]
GTTCAGTTCTTTTTTCCTTTTCCCCTTTTTTTTCCATGTCCCCCAACAATGGCTTTCTAACTGTTTGCGTTATGTCAAAACTCTTCTCCTTCTAATAAAA

Reverse complement sequence

TTTTATTAGAAGGAGAAGAGTTTTGACATAACGCAAACAGTTAGAAAGCCATTGTTGGGGGACATGGAAAAAAAAGGGGAAAAGGAAAAAAGAACTGAAC[T/A]
GTTACGGAAAACTACTTAAAGAAAAATAAAACTCCTATGACGAGGGAGGGTGGAGGCGGAGCCCCACTAAACTCCCAGCAAGTCCTCAATAGCAGCAACA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.60%	19.00%	0.30%	0.11%	NA
All Indica	2759	67.70%	31.70%	0.47%	0.18%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	78.20%	21.80%	0.00%	0.00%	NA
Indica II	465	91.20%	8.60%	0.22%	0.00%	NA
Indica III	913	48.40%	50.30%	0.99%	0.33%	NA
Indica Intermediate	786	68.20%	31.20%	0.38%	0.25%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0809186402	A -> T	LOC_Os08g15180.1	upstream_gene_variant ; 4395.0bp to feature; MODIFIER	silent_mutation	Average:66.596; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0809186402	A -> T	LOC_Os08g15190.1	downstream_gene_variant ; 715.0bp to feature; MODIFIER	silent_mutation	Average:66.596; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0809186402	A -> T	LOC_Os08g15190-LOC_Os08g15204	intergenic_region ; MODIFIER	silent_mutation	Average:66.596; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0809186402	A -> DEL	N	N	silent_mutation	Average:66.596; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809186402	NA	3.62E-07	mr1994_2	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
vg0809186402	NA	1.65E-08	mr1994_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