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Detailed information for vg1222936918:

Variant ID: vg1222936918 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22936918
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTACATGTATGTGCCTATGAGCCATGCATGTACGTGTAGGGGTGGTAATAGTCAAGGCGCATGGGTTGTTTTACAATTCTACCTAGTTCTTAAAAATA[T/A]
TTTTTTAGTTCAAAATGAATAAAAGTTCAACCCACCCGGCCTATTTACACCCAGCTCTTAAATTTTATAGTCTAAAAAGTTGGGTCCTTTACCATCCCTA

Reverse complement sequence

TAGGGATGGTAAAGGACCCAACTTTTTAGACTATAAAATTTAAGAGCTGGGTGTAAATAGGCCGGGTGGGTTGAACTTTTATTCATTTTGAACTAAAAAA[A/T]
TATTTTTAAGAACTAGGTAGAATTGTAAAACAACCCATGCGCCTTGACTATTACCACCCCTACACGTACATGCATGGCTCATAGGCACATACATGTAGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.80%	35.00%	0.11%	0.08%	NA
All Indica	2759	40.90%	58.80%	0.18%	0.14%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	75.10%	24.70%	0.17%	0.00%	NA
Indica II	465	48.20%	51.60%	0.00%	0.22%	NA
Indica III	913	18.30%	81.50%	0.22%	0.00%	NA
Indica Intermediate	786	37.00%	62.30%	0.25%	0.38%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg1222936918	T -> DEL	N	N	silent_mutation	Average:77.669; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg1222936918	T -> A	LOC_Os12g37340.1	upstream_gene_variant ; 2645.0bp to feature; MODIFIER	silent_mutation	Average:77.669; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg1222936918	T -> A	LOC_Os12g37350.1	downstream_gene_variant ; 100.0bp to feature; MODIFIER	silent_mutation	Average:77.669; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg1222936918	T -> A	LOC_Os12g37360.1	downstream_gene_variant ; 2828.0bp to feature; MODIFIER	silent_mutation	Average:77.669; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N
vg1222936918	T -> A	LOC_Os12g37350-LOC_Os12g37360	intergenic_region ; MODIFIER	silent_mutation	Average:77.669; most accessible tissue: Zhenshan97 panicle, score: 92.403	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222936918	NA	6.68E-07	mr1925	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
vg1222936918	NA	3.39E-07	mr1376_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
vg1222936918	NA	6.38E-06	mr1876_2	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
vg1222936918	NA	8.62E-08	mr1925_2	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
vg1222936918	NA	1.59E-06	mr1951_2	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