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Detailed information for vg1114617929:

Variant ID: vg1114617929 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14617929
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTGTTCGCCACTGCACACACCTTTCGCCACTTCATACATCCTTCGTCATGGCTCCCCGCAAGCCTAACCCCTCTTCGGCGAAAGGGCCCGACCCCGGC[C/T]
GGATTGACAACGACACCACCGCCTGTTTAGGGATTTCTCTCATAGACGATGGCGAGCAGGCAAAGTTGGTCAGCTCTGGGGCTTTAGTCGAGGGACAGGC

Reverse complement sequence

GCCTGTCCCTCGACTAAAGCCCCAGAGCTGACCAACTTTGCCTGCTCGCCATCGTCTATGAGAGAAATCCCTAAACAGGCGGTGGTGTCGTTGTCAATCC[G/A]
GCCGGGGTCGGGCCCTTTCGCCGAAGAGGGGTTAGGCTTGCGGGGAGCCATGACGAAGGATGTATGAAGTGGCGAAAGGTGTGTGCAGTGGCGAACAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.60%	2.70%	24.78%	11.87%	NA
All Indica	2759	35.00%	4.60%	42.04%	18.30%	NA
All Japonica	1512	98.90%	0.00%	0.20%	0.86%	NA
Aus	269	91.40%	0.00%	1.12%	7.43%	NA
Indica I	595	41.50%	1.50%	31.76%	25.21%	NA
Indica II	465	9.90%	1.90%	53.55%	34.62%	NA
Indica III	913	44.00%	9.40%	42.94%	3.61%	NA
Indica Intermediate	786	34.50%	3.10%	41.98%	20.48%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	98.00%	0.00%	0.60%	1.39%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	0.00%	5.56%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114617929	C -> T	LOC_Os11g25640.1	upstream_gene_variant ; 386.0bp to feature; MODIFIER	silent_mutation	Average:14.909; most accessible tissue: Callus, score: 42.026	N	N	N	N
vg1114617929	C -> T	LOC_Os11g25630.1	downstream_gene_variant ; 4229.0bp to feature; MODIFIER	silent_mutation	Average:14.909; most accessible tissue: Callus, score: 42.026	N	N	N	N
vg1114617929	C -> T	LOC_Os11g25630-LOC_Os11g25640	intergenic_region ; MODIFIER	silent_mutation	Average:14.909; most accessible tissue: Callus, score: 42.026	N	N	N	N
vg1114617929	C -> DEL	N	N	silent_mutation	Average:14.909; most accessible tissue: Callus, score: 42.026	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114617929	4.64E-06	2.97E-06	mr1158_2	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
vg1114617929	NA	8.04E-08	mr1158_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