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Detailed information for vg0125070140:

Variant ID: vg0125070140 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 25070140
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, A: 0.23, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAAAATATTTATATAAATATAATAAAAGGAAAAGTTACGTTTAAAATAAGTAAGTTGCAAATAAAATAAATAATAATTTTAAAATTTTTTAATAAGAT[A/G]
AATGGTCAAATAGTGCAATTAAAATGTCCCTATAAAGAGGGAGGGAGTACTACCTACCAATGCTAGCAACTCGGATCGGCTTGAACAGATCAACACAAGT

Reverse complement sequence

ACTTGTGTTGATCTGTTCAAGCCGATCCGAGTTGCTAGCATTGGTAGGTAGTACTCCCTCCCTCTTTATAGGGACATTTTAATTGCACTATTTGACCATT[T/C]
ATCTTATTAAAAAATTTTAAAATTATTATTTATTTTATTTGCAACTTACTTATTTTAAACGTAACTTTTCCTTTTATTATATTTATATAAATATTTTAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.70%	13.10%	0.21%	0.00%	NA
All Indica	2759	85.90%	13.80%	0.25%	0.00%	NA
All Japonica	1512	85.30%	14.60%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	78.30%	21.30%	0.34%	0.00%	NA
Indica II	465	91.20%	8.40%	0.43%	0.00%	NA
Indica III	913	89.00%	11.00%	0.00%	0.00%	NA
Indica Intermediate	786	85.00%	14.60%	0.38%	0.00%	NA
Temperate Japonica	767	98.00%	1.70%	0.26%	0.00%	NA
Tropical Japonica	504	70.60%	29.40%	0.00%	0.00%	NA
Japonica Intermediate	241	75.10%	24.90%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg0125070140	A -> G	LOC_Os01g43760.1	upstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:63.154; most accessible tissue: Callus, score: 93.607	N	N	N	N
vg0125070140	A -> G	LOC_Os01g43774.1	upstream_gene_variant ; 3709.0bp to feature; MODIFIER	silent_mutation	Average:63.154; most accessible tissue: Callus, score: 93.607	N	N	N	N
vg0125070140	A -> G	LOC_Os01g43750.1	downstream_gene_variant ; 1841.0bp to feature; MODIFIER	silent_mutation	Average:63.154; most accessible tissue: Callus, score: 93.607	N	N	N	N
vg0125070140	A -> G	LOC_Os01g43750-LOC_Os01g43760	intergenic_region ; MODIFIER	silent_mutation	Average:63.154; most accessible tissue: Callus, score: 93.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0125070140	4.83E-06	4.83E-06	mr1856	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