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Detailed information for vg1020206725:

Variant ID: vg1020206725 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 20206725
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, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTTGGACTAATTCGCGAGACGAATCTATTGAGCCTAATTAATTCATAATTAGCCTATGTGATGCTACAGTAAACATTCTCTAATTATAGATTAATTAG[G/A]
CTTAAAAAATTTGTCTTGCAAATTAGTTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATTTAATACTCTAAATTAGTATATAAATACAGAGACTA

Reverse complement sequence

TAGTCTCTGTATTTATATACTAATTTAGAGTATTAAATATAGACTACTTACAAAACTAATTACATAAATGAAAACTAATTTGCAAGACAAATTTTTTAAG[C/T]
CTAATTAATCTATAATTAGAGAATGTTTACTGTAGCATCACATAGGCTAATTATGAATTAATTAGGCTCAATAGATTCGTCTCGCGAATTAGTCCAAGAT

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	89.50%	10.00%	0.42%	0.04%	NA
All Indica	2759	90.70%	8.70%	0.65%	0.00%	NA
All Japonica	1512	98.70%	1.10%	0.07%	0.13%	NA
Aus	269	30.10%	69.90%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	72.70%	25.60%	1.72%	0.00%	NA
Indica III	913	98.60%	1.30%	0.11%	0.00%	NA
Indica Intermediate	786	85.60%	13.50%	0.89%	0.00%	NA
Temperate Japonica	767	98.30%	1.30%	0.13%	0.26%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	84.40%	14.40%	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
vg1020206725	G -> A	LOC_Os10g37760.1	upstream_gene_variant ; 615.0bp to feature; MODIFIER	silent_mutation	Average:34.346; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1020206725	G -> A	LOC_Os10g37760.2	upstream_gene_variant ; 615.0bp to feature; MODIFIER	silent_mutation	Average:34.346; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1020206725	G -> A	LOC_Os10g37770.1	downstream_gene_variant ; 4228.0bp to feature; MODIFIER	silent_mutation	Average:34.346; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1020206725	G -> A	LOC_Os10g37740-LOC_Os10g37760	intergenic_region ; MODIFIER	silent_mutation	Average:34.346; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1020206725	G -> DEL	N	N	silent_mutation	Average:34.346; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1020206725	NA	3.64E-06	mr1295	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
vg1020206725	NA	1.58E-06	mr1510	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1020206725	NA	7.78E-07	mr1762_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251