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Detailed information for vg1125170215:

Variant ID: vg1125170215 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25170215
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTGTTTGTTAACATGAAAGAAGAGGAAGCTGACTAGTTGGGTTGGACTTGGAAGCAAACATTTATTTTAGGCTCCATTCTAATGCGCAGATTTGGCTA[C/A]
GTTGAGCTGAATTGGTAGCAGTCTAAATAATACTCCCTCTGTCAGAAAAAACCAATCCTGGGTTGATCTAGACATAATGTACGTCCAAATTTAAACCTAG

Reverse complement sequence

CTAGGTTTAAATTTGGACGTACATTATGTCTAGATCAACCCAGGATTGGTTTTTTCTGACAGAGGGAGTATTATTTAGACTGCTACCAATTCAGCTCAAC[G/T]
TAGCCAAATCTGCGCATTAGAATGGAGCCTAAAATAAATGTTTGCTTCCAAGTCCAACCCAACTAGTCAGCTTCCTCTTCTTTCATGTTAACAAACAAAG

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	95.80%	4.10%	0.06%	0.00%	NA
All Indica	2759	93.20%	6.70%	0.07%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	95.70%	4.30%	0.00%	0.00%	NA
Indica III	913	88.30%	11.50%	0.22%	0.00%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1125170215	C -> A	LOC_Os11g41850.1	upstream_gene_variant ; 2469.0bp to feature; MODIFIER	silent_mutation	Average:61.232; most accessible tissue: Callus, score: 91.834	N	N	N	N
vg1125170215	C -> A	LOC_Os11g41860.1	upstream_gene_variant ; 1504.0bp to feature; MODIFIER	silent_mutation	Average:61.232; most accessible tissue: Callus, score: 91.834	N	N	N	N
vg1125170215	C -> A	LOC_Os11g41860.2	upstream_gene_variant ; 1483.0bp to feature; MODIFIER	silent_mutation	Average:61.232; most accessible tissue: Callus, score: 91.834	N	N	N	N
vg1125170215	C -> A	LOC_Os11g41870.1	downstream_gene_variant ; 4799.0bp to feature; MODIFIER	silent_mutation	Average:61.232; most accessible tissue: Callus, score: 91.834	N	N	N	N
vg1125170215	C -> A	LOC_Os11g41850-LOC_Os11g41860	intergenic_region ; MODIFIER	silent_mutation	Average:61.232; most accessible tissue: Callus, score: 91.834	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125170215	4.20E-06	4.20E-06	mr1821_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