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Detailed information for vg1211686189:

Variant ID: vg1211686189 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11686189
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CTCACTAGTAAATCCTCTCTATCCTGGCCTATCAATTGCTTGGTGTCCTTGGATGAACCGGAGGAAGCTCTGATCACACATGTTCCCTTGGATTCGATAC[C/T,A]
CTTGGAATACTCCGTAGGGGAAGTGCTACATCGGTATATCCGTGCGCTTGCGGATTTTATCTGTAACCGTATCAAATACCAACACTAGACTCAGATCAGC

Reverse complement sequence

GCTGATCTGAGTCTAGTGTTGGTATTTGATACGGTTACAGATAAAATCCGCAAGCGCACGGATATACCGATGTAGCACTTCCCCTACGGAGTATTCCAAG[G/A,T]
GTATCGAATCCAAGGGAACATGTGTGATCAGAGCTTCCTCCGGTTCATCCAAGGACACCAAGCAATTGATAGGCCAGGATAGAGAGGATTTACTAGTGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.50%	2.80%	2.48%	2.96%	T: 0.28%
All Indica	2759	97.40%	0.00%	1.81%	0.36%	T: 0.43%
All Japonica	1512	81.50%	6.70%	3.24%	8.47%	NA
Aus	269	87.40%	7.40%	4.83%	0.00%	T: 0.37%
Indica I	595	97.80%	0.00%	2.02%	0.17%	NA
Indica II	465	95.50%	0.20%	3.23%	0.65%	T: 0.43%
Indica III	913	98.70%	0.00%	0.44%	0.22%	T: 0.66%
Indica Intermediate	786	96.60%	0.00%	2.42%	0.51%	T: 0.51%
Temperate Japonica	767	85.90%	1.30%	1.83%	10.95%	NA
Tropical Japonica	504	75.80%	14.10%	4.17%	5.95%	NA
Japonica Intermediate	241	79.70%	8.70%	5.81%	5.81%	NA
VI/Aromatic	96	91.70%	4.20%	4.17%	0.00%	NA
Intermediate	90	93.30%	3.30%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211686189	C -> DEL	N	N	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> A	LOC_Os12g20110.1	upstream_gene_variant ; 4022.0bp to feature; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> A	LOC_Os12g20100.1	downstream_gene_variant ; 419.0bp to feature; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> A	LOC_Os12g20090-LOC_Os12g20100	intergenic_region ; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> T	LOC_Os12g20110.1	upstream_gene_variant ; 4022.0bp to feature; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> T	LOC_Os12g20100.1	downstream_gene_variant ; 419.0bp to feature; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N
vg1211686189	C -> T	LOC_Os12g20090-LOC_Os12g20100	intergenic_region ; MODIFIER	silent_mutation	Average:27.987; most accessible tissue: Zhenshan97 flag leaf, score: 59.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211686189	NA	8.58E-07	mr1531_2	Jap_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