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Detailed information for vg0525443073:

Variant ID: vg0525443073 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 25443073
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AACTTCCAACTTTTCCATCACATCAAAACTTTCCTACACACACAAACTTCCAACTTTTTTGTCACATCGTTCCAATTTCAACCAAACTTCCAATTTTAGC[G/A]
TGAACTAAACACACCTATAGTAGGAATTTGAGATATGGAACTATGTCAGACATGATCTTGCTATACACGGCTCTATAAATAGGTAAAGAAGTGTTTTATA

Reverse complement sequence

TATAAAACACTTCTTTACCTATTTATAGAGCCGTGTATAGCAAGATCATGTCTGACATAGTTCCATATCTCAAATTCCTACTATAGGTGTGTTTAGTTCA[C/T]
GCTAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACAAAAAAGTTGGAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTGGAAGTT

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	93.00%	5.10%	1.93%	0.00%	NA
All Indica	2759	88.30%	8.50%	3.19%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.10%	1.20%	6.72%	0.00%	NA
Indica II	465	83.40%	13.10%	3.44%	0.00%	NA
Indica III	913	87.20%	12.00%	0.77%	0.00%	NA
Indica Intermediate	786	89.60%	7.30%	3.18%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	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
vg0525443073	G -> A	LOC_Os05g43770.1	upstream_gene_variant ; 3813.0bp to feature; MODIFIER	silent_mutation	Average:38.588; most accessible tissue: Callus, score: 60.676	N	N	N	N
vg0525443073	G -> A	LOC_Os05g43760.1	downstream_gene_variant ; 4370.0bp to feature; MODIFIER	silent_mutation	Average:38.588; most accessible tissue: Callus, score: 60.676	N	N	N	N
vg0525443073	G -> A	LOC_Os05g43760-LOC_Os05g43770	intergenic_region ; MODIFIER	silent_mutation	Average:38.588; most accessible tissue: Callus, score: 60.676	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0525443073	1.86E-06	NA	mr1935	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