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Detailed information for vg0809152994:

Variant ID: vg0809152994 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9152994
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATCTTGGATCAGGGGGCGGCTAGCGATGCACGCAAGGATGTGATGGAGAAGTCAGCGATCTGGGGGAATCCGTTCTCCCACTTTTTGAAGAGTAGGGCC[A/G]
CCGTTTGCCTGTACCCCTTAACCAATCGCGCTTTGTACCCCTTAACCAATCGCGCTTTGTAAAACTTTCGTTGGTTCCAACTGCCTTTGTGTATGCAGTT

Reverse complement sequence

AACTGCATACACAAAGGCAGTTGGAACCAACGAAAGTTTTACAAAGCGCGATTGGTTAAGGGGTACAAAGCGCGATTGGTTAAGGGGTACAGGCAAACGG[T/C]
GGCCCTACTCTTCAAAAAGTGGGAGAACGGATTCCCCCAGATCGCTGACTTCTCCATCACATCCTTGCGTGCATCGCTAGCCGCCCCCTGATCCAAGATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.30%	12.00%	0.72%	59.97%	NA
All Indica	2759	35.70%	1.20%	0.25%	62.85%	NA
All Japonica	1512	1.00%	34.50%	1.52%	63.03%	NA
Aus	269	96.30%	0.00%	0.00%	3.72%	NA
Indica I	595	36.00%	2.50%	0.17%	61.34%	NA
Indica II	465	37.00%	1.10%	0.65%	61.29%	NA
Indica III	913	34.00%	0.20%	0.00%	65.83%	NA
Indica Intermediate	786	36.90%	1.30%	0.38%	61.45%	NA
Temperate Japonica	767	0.40%	59.10%	1.69%	38.85%	NA
Tropical Japonica	504	1.40%	1.80%	1.39%	95.44%	NA
Japonica Intermediate	241	2.10%	24.50%	1.24%	72.20%	NA
VI/Aromatic	96	9.40%	0.00%	1.04%	89.58%	NA
Intermediate	90	24.40%	15.60%	3.33%	56.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809152994	A -> G	LOC_Os08g15110.1	downstream_gene_variant ; 1799.0bp to feature; MODIFIER	silent_mutation	Average:54.291; most accessible tissue: Zhenshan97 flower, score: 68.734	N	N	N	N
vg0809152994	A -> G	LOC_Os08g15120.1	downstream_gene_variant ; 3303.0bp to feature; MODIFIER	silent_mutation	Average:54.291; most accessible tissue: Zhenshan97 flower, score: 68.734	N	N	N	N
vg0809152994	A -> G	LOC_Os08g15100.1	intron_variant ; MODIFIER	silent_mutation	Average:54.291; most accessible tissue: Zhenshan97 flower, score: 68.734	N	N	N	N
vg0809152994	A -> DEL	N	N	silent_mutation	Average:54.291; most accessible tissue: Zhenshan97 flower, score: 68.734	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809152994	4.43E-06	NA	mr1390_2	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
vg0809152994	5.79E-07	NA	mr1490_2	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