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Detailed information for vg1106471446:

Variant ID: vg1106471446 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6471446
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, C: 0.36, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

AAAAAAGTGGGGGCAAAAAGAAAACCTTAAAAAAATATGGGCAAAATCAATATTGAGATGAAAGTGAGGGCAAAAACAAAGTTGTCCCTAACAAATTTGA[G/C]
TATGACTTATGCGTTTTATTCATAGTTAAATTTATTGTTTTTGTTTCTATTTGTACAGGTTGAATTGAACCTACTTTCTCTATCCCATAAAAATCAACCT

Reverse complement sequence

AGGTTGATTTTTATGGGATAGAGAAAGTAGGTTCAATTCAACCTGTACAAATAGAAACAAAAACAATAAATTTAACTATGAATAAAACGCATAAGTCATA[C/G]
TCAAATTTGTTAGGGACAACTTTGTTTTTGCCCTCACTTTCATCTCAATATTGATTTTGCCCATATTTTTTTAAGGTTTTCTTTTTGCCCCCACTTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.70%	44.80%	1.63%	0.93%	NA
All Indica	2759	81.30%	14.50%	2.57%	1.56%	NA
All Japonica	1512	9.30%	90.70%	0.07%	0.00%	NA
Aus	269	16.00%	83.60%	0.37%	0.00%	NA
Indica I	595	90.80%	5.20%	3.19%	0.84%	NA
Indica II	465	96.80%	1.70%	1.51%	0.00%	NA
Indica III	913	66.90%	26.60%	3.72%	2.74%	NA
Indica Intermediate	786	81.80%	15.10%	1.40%	1.65%	NA
Temperate Japonica	767	6.00%	94.00%	0.00%	0.00%	NA
Tropical Japonica	504	11.50%	88.30%	0.20%	0.00%	NA
Japonica Intermediate	241	14.90%	85.10%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	55.60%	38.90%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106471446	G -> DEL	N	N	silent_mutation	Average:29.062; most accessible tissue: Callus, score: 63.294	N	N	N	N
vg1106471446	G -> C	LOC_Os11g11640.1	upstream_gene_variant ; 1886.0bp to feature; MODIFIER	silent_mutation	Average:29.062; most accessible tissue: Callus, score: 63.294	N	N	N	N
vg1106471446	G -> C	LOC_Os11g11630.1	downstream_gene_variant ; 99.0bp to feature; MODIFIER	silent_mutation	Average:29.062; most accessible tissue: Callus, score: 63.294	N	N	N	N
vg1106471446	G -> C	LOC_Os11g11620-LOC_Os11g11630	intergenic_region ; MODIFIER	silent_mutation	Average:29.062; most accessible tissue: Callus, score: 63.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106471446	NA	1.44E-07	mr1836	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
vg1106471446	5.26E-07	5.25E-07	mr1520_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