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Detailed information for vg0225140996:

Variant ID: vg0225140996 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25140996
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TTTACTCGACCACTTTTTTTTTTAACGAATTGGTAAGCTGCCAATTTCATTGAATAGAGAATGGAGAAAACTTTACTAGTACGAAAGGAAACACAGCTCC[G/A]
GACCTTTGGTCCAGATGAGCTAAGAAATTAAAAAGCTAGCCAGCTACCAAGATGTCTCGCACTAGCCAATGACCACGTTTTGGCCTTCTCTTTGATTTTA

Reverse complement sequence

TAAAATCAAAGAGAAGGCCAAAACGTGGTCATTGGCTAGTGCGAGACATCTTGGTAGCTGGCTAGCTTTTTAATTTCTTAGCTCATCTGGACCAAAGGTC[C/T]
GGAGCTGTGTTTCCTTTCGTACTAGTAAAGTTTTCTCCATTCTCTATTCAATGAAATTGGCAGCTTACCAATTCGTTAAAAAAAAAAGTGGTCGAGTAAA

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	63.20%	36.10%	0.72%	0.00%	NA
All Indica	2759	76.30%	23.50%	0.14%	0.00%	NA
All Japonica	1512	38.60%	59.60%	1.85%	0.00%	NA
Aus	269	69.90%	30.10%	0.00%	0.00%	NA
Indica I	595	75.10%	24.50%	0.34%	0.00%	NA
Indica II	465	71.00%	29.00%	0.00%	0.00%	NA
Indica III	913	83.00%	17.00%	0.00%	0.00%	NA
Indica Intermediate	786	72.60%	27.10%	0.25%	0.00%	NA
Temperate Japonica	767	51.80%	45.20%	3.00%	0.00%	NA
Tropical Japonica	504	26.80%	73.20%	0.00%	0.00%	NA
Japonica Intermediate	241	21.20%	76.80%	2.07%	0.00%	NA
VI/Aromatic	96	62.50%	37.50%	0.00%	0.00%	NA
Intermediate	90	55.60%	42.20%	2.22%	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
vg0225140996	G -> A	LOC_Os02g41810.1	upstream_gene_variant ; 4466.0bp to feature; MODIFIER	silent_mutation	Average:50.104; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0225140996	G -> A	LOC_Os02g41800.1	downstream_gene_variant ; 4885.0bp to feature; MODIFIER	silent_mutation	Average:50.104; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0225140996	G -> A	LOC_Os02g41800.2	downstream_gene_variant ; 4885.0bp to feature; MODIFIER	silent_mutation	Average:50.104; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N
vg0225140996	G -> A	LOC_Os02g41800-LOC_Os02g41810	intergenic_region ; MODIFIER	silent_mutation	Average:50.104; most accessible tissue: Minghui63 root, score: 76.119	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225140996	4.78E-06	4.76E-06	mr1597	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