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Detailed information for vg0224866249:

Variant ID: vg0224866249 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24866249
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCGTTTGTTGCCCAATCAGATGAACAACTTTGACAATGGAACTGCGGTGCTCTAAGAAGTAATTTAGGCTTTCTATAATATATGTAAATTACTTTTAG[G/A]
CTTTATTGAATTTACTTTTATATGTCTAAGAAGTAATTTAGTGAAATCTAAGAAGTAATTTAGATATTTTATAAAAGTAATTTATATTTTTTCATCAAAA

Reverse complement sequence

TTTTGATGAAAAAATATAAATTACTTTTATAAAATATCTAAATTACTTCTTAGATTTCACTAAATTACTTCTTAGACATATAAAAGTAAATTCAATAAAG[C/T]
CTAAAAGTAATTTACATATATTATAGAAAGCCTAAATTACTTCTTAGAGCACCGCAGTTCCATTGTCAAAGTTGTTCATCTGATTGGGCAACAAACGGAC

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	82.50%	2.10%	4.59%	10.77%	NA
All Indica	2759	74.70%	0.90%	6.92%	17.51%	NA
All Japonica	1512	92.00%	5.00%	1.59%	1.46%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	66.20%	0.80%	10.42%	22.52%	NA
Indica II	465	74.40%	1.50%	9.03%	15.05%	NA
Indica III	913	84.10%	0.30%	1.75%	13.80%	NA
Indica Intermediate	786	70.20%	1.30%	9.03%	19.47%	NA
Temperate Japonica	767	93.70%	4.00%	1.69%	0.52%	NA
Tropical Japonica	504	94.40%	0.40%	1.79%	3.37%	NA
Japonica Intermediate	241	81.30%	17.40%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	1.10%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224866249	G -> A	LOC_Os02g41480.1	upstream_gene_variant ; 1450.0bp to feature; MODIFIER	silent_mutation	Average:74.69; most accessible tissue: Zhenshan97 root, score: 88.778	N	N	N	N
vg0224866249	G -> A	LOC_Os02g41490.1	downstream_gene_variant ; 522.0bp to feature; MODIFIER	silent_mutation	Average:74.69; most accessible tissue: Zhenshan97 root, score: 88.778	N	N	N	N
vg0224866249	G -> A	LOC_Os02g41480-LOC_Os02g41490	intergenic_region ; MODIFIER	silent_mutation	Average:74.69; most accessible tissue: Zhenshan97 root, score: 88.778	N	N	N	N
vg0224866249	G -> DEL	N	N	silent_mutation	Average:74.69; most accessible tissue: Zhenshan97 root, score: 88.778	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224866249	2.86E-06	2.86E-06	mr1015	Jap_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