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Detailed information for vg1125839534:

Variant ID: vg1125839534 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25839534
Reference Allele: C	Alternative Allele: T,A
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, C: 0.23, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

GGTATAAATAGAGGGAGAGGGTATGGCCTCCCGGTATCGGTTGTAAGTGAGGCAAATTTGAGAGATTAGATAGGGTTTCGTAAGAAACTTGTAAGGGGTG[C/T,A]
TGTGGCTGCACCTTGTGAACAATACTTGAATAATAAAGATCATATTCAATCATCAAGGTATCGACGATCTATTTCGGTTTTGTAAGTTTTACGTTTATGT

Reverse complement sequence

ACATAAACGTAAAACTTACAAAACCGAAATAGATCGTCGATACCTTGATGATTGAATATGATCTTTATTATTCAAGTATTGTTCACAAGGTGCAGCCACA[G/A,T]
CACCCCTTACAAGTTTCTTACGAAACCCTATCTAATCTCTCAAATTTGCCTCACTTACAACCGATACCGGGAGGCCATACCCTCTCCCTCTATTTATACC

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	57.40%	39.00%	1.18%	2.41%	NA
All Indica	2759	58.60%	35.80%	1.78%	3.88%	NA
All Japonica	1512	56.00%	43.90%	0.00%	0.07%	NA
Aus	269	51.30%	45.40%	1.49%	1.86%	NA
Indica I	595	81.50%	10.90%	3.36%	4.20%	NA
Indica II	465	37.00%	52.50%	1.72%	8.82%	NA
Indica III	913	61.00%	37.20%	0.55%	1.20%	NA
Indica Intermediate	786	51.10%	43.00%	2.04%	3.82%	NA
Temperate Japonica	767	79.00%	20.90%	0.00%	0.13%	NA
Tropical Japonica	504	23.80%	76.20%	0.00%	0.00%	NA
Japonica Intermediate	241	50.20%	49.80%	0.00%	0.00%	NA
VI/Aromatic	96	52.10%	45.80%	2.08%	0.00%	NA
Intermediate	90	71.10%	26.70%	1.11%	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
vg1125839534	C -> T	LOC_Os11g42890.1	upstream_gene_variant ; 2836.0bp to feature; MODIFIER	silent_mutation	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> T	LOC_Os11g42900.1	downstream_gene_variant ; 1059.0bp to feature; MODIFIER	silent_mutation	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> T	LOC_Os11g42890-LOC_Os11g42900	intergenic_region ; MODIFIER	silent_mutation	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> A	LOC_Os11g42890.1	upstream_gene_variant ; 2836.0bp to feature; MODIFIER	N	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> A	LOC_Os11g42900.1	downstream_gene_variant ; 1059.0bp to feature; MODIFIER	N	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> A	LOC_Os11g42890-LOC_Os11g42900	intergenic_region ; MODIFIER	N	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N
vg1125839534	C -> DEL	N	N	silent_mutation	Average:45.099; most accessible tissue: Callus, score: 66.297	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125839534	1.16E-06	NA	mr1191	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
vg1125839534	6.64E-06	2.12E-07	mr1191	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
vg1125839534	2.60E-10	1.55E-10	mr1644	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
vg1125839534	1.51E-08	2.76E-12	mr1644	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
vg1125839534	2.11E-06	NA	mr1191_2	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
vg1125839534	NA	3.02E-10	mr1191_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