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Detailed information for vg0800440463:

Variant ID: vg0800440463 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 440463
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

GAGAGAAAGGATGACATGTGGGCCCCCCACATGTCAATGGGTCCCACGATATGAATGACAGATGGGTCCCACTATTTTTTTTTAATTCTAATGCCACTTA[A/T]
GCGCCACGTGGGACGAAAACCGGGTCAACACCGTCATGTCAGCGCCACGTCAGCAAAACCGCCCTCCAATACCGCTGAGGGAGTCAAATTGCACCGGTTT

Reverse complement sequence

AAACCGGTGCAATTTGACTCCCTCAGCGGTATTGGAGGGCGGTTTTGCTGACGTGGCGCTGACATGACGGTGTTGACCCGGTTTTCGTCCCACGTGGCGC[T/A]
TAAGTGGCATTAGAATTAAAAAAAAATAGTGGGACCCATCTGTCATTCATATCGTGGGACCCATTGACATGTGGGGGGCCCACATGTCATCCTTTCTCTC

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	38.60%	0.10%	39.80%	21.43%	NA
All Indica	2759	9.60%	0.30%	61.65%	28.49%	NA
All Japonica	1512	97.40%	0.00%	0.26%	2.31%	NA
Aus	269	4.80%	0.00%	56.51%	38.66%	NA
Indica I	595	11.40%	0.70%	40.84%	47.06%	NA
Indica II	465	10.80%	0.00%	59.78%	29.46%	NA
Indica III	913	4.80%	0.00%	80.83%	14.35%	NA
Indica Intermediate	786	13.10%	0.40%	56.23%	30.28%	NA
Temperate Japonica	767	98.70%	0.00%	0.13%	1.17%	NA
Tropical Japonica	504	95.40%	0.00%	0.00%	4.56%	NA
Japonica Intermediate	241	97.50%	0.00%	1.24%	1.24%	NA
VI/Aromatic	96	26.00%	0.00%	7.29%	66.67%	NA
Intermediate	90	54.40%	0.00%	18.89%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0800440463	A -> T	LOC_Os08g01710.1	upstream_gene_variant ; 3429.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800440463	A -> T	LOC_Os08g01720.1	downstream_gene_variant ; 692.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800440463	A -> T	LOC_Os08g01720-LOC_Os08g01740	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0800440463	A -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800440463	3.81E-06	7.41E-07	mr1508_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
vg0800440463	NA	8.94E-07	mr1655_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