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Detailed information for vg0808663101:

Variant ID: vg0808663101 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8663101
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTCTCCTCCCCTTCTTCTCTTCCTATTACAGTACACCACACAAAATTTTTTTAAAAAACAAAAAGTTAGAAAAATTTATGTATAGAAATACTATATATA[A/T]
AAAATTTGAATTCAAATTTGAATCGGGTATGTAAACGTTTGACTTATAAACTTTGGGTCTATAAACTTTAGGTGTATAAACTTTTAGTTGTATAGAAATA

Reverse complement sequence

TATTTCTATACAACTAAAAGTTTATACACCTAAAGTTTATAGACCCAAAGTTTATAAGTCAAACGTTTACATACCCGATTCAAATTTGAATTCAAATTTT[T/A]
TATATATAGTATTTCTATACATAAATTTTTCTAACTTTTTGTTTTTTAAAAAAATTTTGTGTGGTGTACTGTAATAGGAAGAGAAGAAGGGGAGGAGAAA

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	89.10%	10.30%	0.38%	0.15%	NA
All Indica	2759	99.50%	0.30%	0.11%	0.07%	NA
All Japonica	1512	67.80%	30.90%	0.99%	0.33%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	98.90%	0.40%	0.22%	0.43%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	86.60%	12.10%	0.78%	0.52%	NA
Tropical Japonica	504	44.80%	53.40%	1.59%	0.20%	NA
Japonica Intermediate	241	56.00%	43.60%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0808663101	A -> T	LOC_Os08g14430-LOC_Os08g14440	intergenic_region ; MODIFIER	silent_mutation	Average:59.513; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0808663101	A -> DEL	N	N	silent_mutation	Average:59.513; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808663101	5.74E-06	NA	mr1117_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
vg0808663101	NA	8.50E-06	mr1329_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
vg0808663101	NA	1.28E-06	mr1524_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
vg0808663101	1.44E-06	2.01E-13	mr1851_2	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
vg0808663101	NA	3.58E-06	mr1851_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