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Detailed information for vg0224875472:

Variant ID: vg0224875472 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24875472
Reference Allele: G	Alternative Allele: A,C
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGTCAAATTAAACCGGTTAGGTACGAATTATGACATATATTTGAGGAAGCGATTTTTCTATATCTCACTCGAAAGATTTTTTTTCTTATCTCTCACTC[G/A,C]
ATTTTTTCACTCAAATTTACAGTGCATTTTCTTGTAAGTTACAGTGTAATTTTTGAATCTTCGCATGCAAATTTTGAAATTTATATTGGATTTGGTCTTT

Reverse complement sequence

AAAGACCAAATCCAATATAAATTTCAAAATTTGCATGCGAAGATTCAAAAATTACACTGTAACTTACAAGAAAATGCACTGTAAATTTGAGTGAAAAAAT[C/T,G]
GAGTGAGAGATAAGAAAAAAAATCTTTCGAGTGAGATATAGAAAAATCGCTTCCTCAAATATATGTCATAATTCGTACCTAACCGGTTTAATTTGACTCT

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	79.20%	20.00%	0.57%	0.00%	C: 0.23%
All Indica	2759	73.60%	25.80%	0.54%	0.00%	NA
All Japonica	1512	97.70%	1.10%	0.46%	0.00%	C: 0.73%
Aus	269	49.40%	48.70%	1.86%	0.00%	NA
Indica I	595	61.20%	38.70%	0.17%	0.00%	NA
Indica II	465	71.60%	28.40%	0.00%	0.00%	NA
Indica III	913	79.30%	20.00%	0.66%	0.00%	NA
Indica Intermediate	786	77.60%	21.40%	1.02%	0.00%	NA
Temperate Japonica	767	99.50%	0.00%	0.52%	0.00%	NA
Tropical Japonica	504	95.60%	1.80%	0.40%	0.00%	C: 2.18%
Japonica Intermediate	241	96.30%	3.30%	0.41%	0.00%	NA
VI/Aromatic	96	35.40%	64.60%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	0.00%	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
vg0224875472	G -> A	LOC_Os02g41500.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N
vg0224875472	G -> A	LOC_Os02g41510.1	downstream_gene_variant ; 3303.0bp to feature; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N
vg0224875472	G -> A	LOC_Os02g41500-LOC_Os02g41510	intergenic_region ; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N
vg0224875472	G -> C	LOC_Os02g41500.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N
vg0224875472	G -> C	LOC_Os02g41510.1	downstream_gene_variant ; 3303.0bp to feature; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N
vg0224875472	G -> C	LOC_Os02g41500-LOC_Os02g41510	intergenic_region ; MODIFIER	silent_mutation	Average:32.284; most accessible tissue: Callus, score: 57.502	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224875472	4.74E-06	NA	mr1183_2	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