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Detailed information for vg1125819922:

Variant ID: vg1125819922 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25819922
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.87, T: 0.14, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTGGCTAGGGAGCAAATCGATGACCTCGTGCATCTCCATCAATCTCCTCACTAGCGTCGTCGAGCTCTGATTGGGGAGCAAATAAGCAACCTCACGGG[C/T]
GTCGTCGAGATGCTCCTCACCAACCTATCATAGTCTTAGGCATGCACGCACACTACAACAAAAACCTCATATAGAGGCACTTTTGTAGAGACGTTTTGCA

Reverse complement sequence

TGCAAAACGTCTCTACAAAAGTGCCTCTATATGAGGTTTTTGTTGTAGTGTGCGTGCATGCCTAAGACTATGATAGGTTGGTGAGGAGCATCTCGACGAC[G/A]
CCCGTGAGGTTGCTTATTTGCTCCCCAATCAGAGCTCGACGACGCTAGTGAGGAGATTGATGGAGATGCACGAGGTCATCGATTTGCTCCCTAGCCAAGG

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	62.00%	37.50%	0.51%	0.00%	NA
All Indica	2759	44.50%	54.90%	0.62%	0.00%	NA
All Japonica	1512	93.50%	6.50%	0.00%	0.00%	NA
Aus	269	54.60%	45.40%	0.00%	0.00%	NA
Indica I	595	57.60%	41.80%	0.50%	0.00%	NA
Indica II	465	21.10%	78.30%	0.65%	0.00%	NA
Indica III	913	49.30%	49.80%	0.88%	0.00%	NA
Indica Intermediate	786	42.70%	56.90%	0.38%	0.00%	NA
Temperate Japonica	767	94.80%	5.20%	0.00%	0.00%	NA
Tropical Japonica	504	91.30%	8.70%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	14.60%	4.17%	0.00%	NA
Intermediate	90	71.10%	25.60%	3.33%	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
vg1125819922	C -> T	LOC_Os11g42860.1	upstream_gene_variant ; 1904.0bp to feature; MODIFIER	silent_mutation	Average:38.837; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1125819922	C -> T	LOC_Os11g42870.1	downstream_gene_variant ; 2873.0bp to feature; MODIFIER	silent_mutation	Average:38.837; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg1125819922	C -> T	LOC_Os11g42860-LOC_Os11g42870	intergenic_region ; MODIFIER	silent_mutation	Average:38.837; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125819922	1.89E-07	2.49E-12	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
vg1125819922	1.33E-06	3.25E-11	mr1609	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
vg1125819922	6.40E-08	6.22E-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
vg1125819922	2.11E-14	9.41E-19	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
vg1125819922	1.47E-11	5.53E-08	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
vg1125819922	NA	2.56E-06	mr1662_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