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Detailed information for vg1221429605:

Variant ID: vg1221429605 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21429605
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.24, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATATACATTTCAATGCTAGTTTAGAAAAGAGATTAGTATTAAGTTTGGCCTAATTCTCAAACTCAAACATCTCCATTGAGATATTATATATCAAGAT[A/G]
CTCCTAGCATGAATTAGCACTGGTATCATCACTGGCAATCCAGTCATCTCTGTTTCTTTATTATCCAATCATCTTGCATCGTATGAGAGAGAAACCAAAA

Reverse complement sequence

TTTTGGTTTCTCTCTCATACGATGCAAGATGATTGGATAATAAAGAAACAGAGATGACTGGATTGCCAGTGATGATACCAGTGCTAATTCATGCTAGGAG[T/C]
ATCTTGATATATAATATCTCAATGGAGATGTTTGAGTTTGAGAATTAGGCCAAACTTAATACTAATCTCTTTTCTAAACTAGCATTGAAATGTATATAAA

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	73.70%	26.20%	0.04%	0.00%	NA
All Indica	2759	72.30%	27.60%	0.04%	0.00%	NA
All Japonica	1512	84.30%	15.70%	0.00%	0.00%	NA
Aus	269	33.80%	65.80%	0.37%	0.00%	NA
Indica I	595	84.50%	15.50%	0.00%	0.00%	NA
Indica II	465	91.00%	9.00%	0.00%	0.00%	NA
Indica III	913	53.70%	46.20%	0.11%	0.00%	NA
Indica Intermediate	786	73.80%	26.20%	0.00%	0.00%	NA
Temperate Japonica	767	86.80%	13.20%	0.00%	0.00%	NA
Tropical Japonica	504	79.80%	20.20%	0.00%	0.00%	NA
Japonica Intermediate	241	85.50%	14.50%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	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
vg1221429605	A -> G	LOC_Os12g35260.1	upstream_gene_variant ; 1476.0bp to feature; MODIFIER	silent_mutation	Average:66.351; most accessible tissue: Zhenshan97 root, score: 83.259	N	N	N	N
vg1221429605	A -> G	LOC_Os12g35280.1	upstream_gene_variant ; 2818.0bp to feature; MODIFIER	silent_mutation	Average:66.351; most accessible tissue: Zhenshan97 root, score: 83.259	N	N	N	N
vg1221429605	A -> G	LOC_Os12g35270.1	downstream_gene_variant ; 29.0bp to feature; MODIFIER	silent_mutation	Average:66.351; most accessible tissue: Zhenshan97 root, score: 83.259	N	N	N	N
vg1221429605	A -> G	LOC_Os12g35260-LOC_Os12g35270	intergenic_region ; MODIFIER	silent_mutation	Average:66.351; most accessible tissue: Zhenshan97 root, score: 83.259	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221429605	NA	4.49E-06	mr1195	Ind_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
vg1221429605	NA	7.60E-06	mr1236	Ind_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
vg1221429605	5.46E-06	NA	mr1397	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
vg1221429605	NA	5.00E-06	mr1743	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