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Detailed information for vg1124410475:

Variant ID: vg1124410475 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24410475
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.16, others allele: 0.00, population size: 62. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTTATTTTTTTTAAAAAAAGACATGCATGAAAATTTGATCAGTTAATTTTTGCCATGTTTGATGTGGCTCAGATCCACTTACTTCGTGCCACACCCAT[T/C]
ATCTCCATCAGTCATCCCCAAATCCAACCAGAGCTCGAGCTCGCCACGGATGACCCACCACCACCACCCATGCACGCATGGATGACGACAAGCTCGCCCT

Reverse complement sequence

AGGGCGAGCTTGTCGTCATCCATGCGTGCATGGGTGGTGGTGGTGGGTCATCCGTGGCGAGCTCGAGCTCTGGTTGGATTTGGGGATGACTGATGGAGAT[A/G]
ATGGGTGTGGCACGAAGTAAGTGGATCTGAGCCACATCAAACATGGCAAAAATTAACTGATCAAATTTTCATGCATGTCTTTTTTTAAAAAAAATAAACT

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	47.60%	23.80%	9.59%	19.04%	NA
All Indica	2759	58.30%	10.40%	11.78%	19.46%	NA
All Japonica	1512	35.50%	43.90%	3.51%	17.06%	NA
Aus	269	16.70%	44.60%	20.45%	18.22%	NA
Indica I	595	71.90%	7.60%	10.59%	9.92%	NA
Indica II	465	54.40%	11.20%	14.62%	19.78%	NA
Indica III	913	55.80%	11.10%	8.11%	25.08%	NA
Indica Intermediate	786	53.30%	11.50%	15.27%	19.97%	NA
Temperate Japonica	767	62.60%	20.30%	4.56%	12.52%	NA
Tropical Japonica	504	4.00%	68.30%	1.98%	25.79%	NA
Japonica Intermediate	241	15.40%	68.00%	3.32%	13.28%	NA
VI/Aromatic	96	14.60%	26.00%	12.50%	46.88%	NA
Intermediate	90	50.00%	28.90%	8.89%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124410475	T -> DEL	N	N	silent_mutation	Average:32.439; most accessible tissue: Callus, score: 54.002	N	N	N	N
vg1124410475	T -> C	LOC_Os11g40800.1	upstream_gene_variant ; 4173.0bp to feature; MODIFIER	silent_mutation	Average:32.439; most accessible tissue: Callus, score: 54.002	N	N	N	N
vg1124410475	T -> C	LOC_Os11g40790-LOC_Os11g40800	intergenic_region ; MODIFIER	silent_mutation	Average:32.439; most accessible tissue: Callus, score: 54.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124410475	NA	1.19E-06	mr1309	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
vg1124410475	3.30E-06	NA	mr1238_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
vg1124410475	NA	7.71E-07	mr1398_2	Jap_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
vg1124410475	NA	1.11E-06	mr1566_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
vg1124410475	4.69E-07	NA	mr1609_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
vg1124410475	NA	1.56E-08	mr1609_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
vg1124410475	NA	2.12E-07	mr1696_2	Jap_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
vg1124410475	1.72E-06	NA	mr1841_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
vg1124410475	6.28E-07	NA	mr1900_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
vg1124410475	NA	2.36E-06	mr1959_2	Jap_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