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Detailed information for vg1122669913:

Variant ID: vg1122669913 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22669913
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

TGAATATAATGGGTCCACCAACTTTATTAAAAATTAAGGGCTAGATGTTTTGCTTTTTTCTCAGAATTTATTGGATTTCTCTATTTTTTATAGAGCGCCA[T/C]
GTGGCAGCCTGAGAGTGTTTATAGGAAGTTTAATGGACTTTTAGTATATAACTAGGAAGGTAGCCCGCGCAGTTGCGCGGGCATATTATTTAAACTATCA

Reverse complement sequence

TGATAGTTTAAATAATATGCCCGCGCAACTGCGCGGGCTACCTTCCTAGTTATATACTAAAAGTCCATTAAACTTCCTATAAACACTCTCAGGCTGCCAC[A/G]
TGGCGCTCTATAAAAAATAGAGAAATCCAATAAATTCTGAGAAAAAAGCAAAACATCTAGCCCTTAATTTTTAATAAAGTTGGTGGACCCATTATATTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.70%	3.50%	9.69%	22.07%	NA
All Indica	2759	56.10%	4.40%	10.47%	29.03%	NA
All Japonica	1512	86.90%	0.60%	4.89%	7.61%	NA
Aus	269	51.30%	2.60%	12.64%	33.46%	NA
Indica I	595	77.30%	1.80%	4.03%	16.81%	NA
Indica II	465	15.50%	8.20%	13.55%	62.80%	NA
Indica III	913	61.40%	3.40%	14.35%	20.81%	NA
Indica Intermediate	786	57.80%	5.30%	9.03%	27.86%	NA
Temperate Japonica	767	87.40%	0.90%	6.13%	5.61%	NA
Tropical Japonica	504	90.10%	0.00%	2.18%	7.74%	NA
Japonica Intermediate	241	78.80%	0.80%	6.64%	13.69%	NA
VI/Aromatic	96	12.50%	19.80%	46.88%	20.83%	NA
Intermediate	90	54.40%	8.90%	17.78%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122669913	T -> DEL	N	N	silent_mutation	Average:52.671; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1122669913	T -> C	LOC_Os11g38270.1	upstream_gene_variant ; 4918.0bp to feature; MODIFIER	silent_mutation	Average:52.671; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1122669913	T -> C	LOC_Os11g38280.1	upstream_gene_variant ; 3622.0bp to feature; MODIFIER	silent_mutation	Average:52.671; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1122669913	T -> C	LOC_Os11g38300.1	downstream_gene_variant ; 2763.0bp to feature; MODIFIER	silent_mutation	Average:52.671; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1122669913	T -> C	LOC_Os11g38280-LOC_Os11g38300	intergenic_region ; MODIFIER	silent_mutation	Average:52.671; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122669913	8.97E-07	8.97E-07	mr1388	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