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Detailed information for vg1221081688:

Variant ID: vg1221081688 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21081688
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAACATACTACTTTTAAAAAGTACATACTTATACTGCAAAACAAGTATATATACTTCTACAACAAGTAGCTAAGTATATACTTTTAATGAGAAAAAAA[G/T]
GTATATACTTCCAACGAGCTACCATTAAATTTTTTGAACCTAGTCGTACGTACGCACCGGCCGGTGCATGCAGATAATTTGAAAAAAAAACAGGAATGGT

Reverse complement sequence

ACCATTCCTGTTTTTTTTTCAAATTATCTGCATGCACCGGCCGGTGCGTACGTACGACTAGGTTCAAAAAATTTAATGGTAGCTCGTTGGAAGTATATAC[C/A]
TTTTTTTCTCATTAAAAGTATATACTTAGCTACTTGTTGTAGAAGTATATATACTTGTTTTGCAGTATAAGTATGTACTTTTTAAAAGTAGTATGTTAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.20%	6.50%	1.48%	2.81%	NA
All Indica	2759	96.10%	0.20%	0.58%	3.12%	NA
All Japonica	1512	76.60%	17.90%	3.04%	2.45%	NA
Aus	269	87.40%	8.20%	2.23%	2.23%	NA
Indica I	595	99.30%	0.00%	0.34%	0.34%	NA
Indica II	465	95.50%	0.20%	1.08%	3.23%	NA
Indica III	913	93.80%	0.20%	0.77%	5.26%	NA
Indica Intermediate	786	96.70%	0.40%	0.25%	2.67%	NA
Temperate Japonica	767	79.50%	17.10%	0.65%	2.74%	NA
Tropical Japonica	504	81.90%	12.30%	3.97%	1.79%	NA
Japonica Intermediate	241	56.00%	32.40%	8.71%	2.90%	NA
VI/Aromatic	96	95.80%	2.10%	1.04%	1.04%	NA
Intermediate	90	88.90%	6.70%	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
vg1221081688	G -> DEL	N	N	silent_mutation	Average:27.585; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg1221081688	G -> T	LOC_Os12g34720.1	upstream_gene_variant ; 1201.0bp to feature; MODIFIER	silent_mutation	Average:27.585; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N
vg1221081688	G -> T	LOC_Os12g34710-LOC_Os12g34720	intergenic_region ; MODIFIER	silent_mutation	Average:27.585; most accessible tissue: Zhenshan97 root, score: 59.664	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221081688	5.72E-07	NA	mr1100_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
vg1221081688	1.07E-06	NA	mr1613_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