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Detailed information for vg1221698417:

Variant ID: vg1221698417 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21698417
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.28, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

ACCACGGTTGAATCATTAAGTATTTTAAAGACACCATGGATCTAAATTTAAATGTGTTCGCAAATTTGATGATTAAGATAAATCTAGTAGAGCTTAGCAG[G/A]
ATGAAAACAGGTGCACACCCTCATTTGTAGCAGACCTAATGCTAATTGCATTGATAATCCCTAGCAAGAATAGGTTAGTCTATTTGGATAACCACATTAA

Reverse complement sequence

TTAATGTGGTTATCCAAATAGACTAACCTATTCTTGCTAGGGATTATCAATGCAATTAGCATTAGGTCTGCTACAAATGAGGGTGTGCACCTGTTTTCAT[C/T]
CTGCTAAGCTCTACTAGATTTATCTTAATCATCAAATTTGCGAACACATTTAAATTTAGATCCATGGTGTCTTTAAAATACTTAATGATTCAACCGTGGT

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	70.40%	25.30%	4.27%	0.00%	NA
All Indica	2759	61.30%	34.50%	4.17%	0.00%	NA
All Japonica	1512	95.20%	4.70%	0.13%	0.00%	NA
Aus	269	21.20%	50.20%	28.62%	0.00%	NA
Indica I	595	39.30%	56.60%	4.03%	0.00%	NA
Indica II	465	94.00%	5.20%	0.86%	0.00%	NA
Indica III	913	51.80%	41.90%	6.24%	0.00%	NA
Indica Intermediate	786	69.60%	26.60%	3.82%	0.00%	NA
Temperate Japonica	767	96.70%	3.30%	0.00%	0.00%	NA
Tropical Japonica	504	91.90%	7.70%	0.40%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	67.70%	26.00%	6.25%	0.00%	NA
Intermediate	90	83.30%	14.40%	2.22%	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
vg1221698417	G -> A	LOC_Os12g35680.1	upstream_gene_variant ; 2819.0bp to feature; MODIFIER	silent_mutation	Average:30.359; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1221698417	G -> A	LOC_Os12g35690.1	upstream_gene_variant ; 1441.0bp to feature; MODIFIER	silent_mutation	Average:30.359; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1221698417	G -> A	LOC_Os12g35700.1	downstream_gene_variant ; 4008.0bp to feature; MODIFIER	silent_mutation	Average:30.359; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N
vg1221698417	G -> A	LOC_Os12g35680-LOC_Os12g35690	intergenic_region ; MODIFIER	silent_mutation	Average:30.359; most accessible tissue: Zhenshan97 root, score: 50.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221698417	9.66E-07	NA	mr1141	Ind_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
vg1221698417	NA	1.58E-06	mr1662	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