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Detailed information for vg1124963993:

Variant ID: vg1124963993 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24963993
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTTTATTTGTTTTTCCAATACTTATCAGACATAAAACAAATGATGAGATTCATTTTTTAGTAAATTACACTTTGGTCCAGCTTTTATTACCCAAGTTT[T/C]
ACTCTGGACCCCCCCCTAAATCTATCTTTTCAATTTGGACCGGATAAATTTACCATTGTTGCGGTTTGGACTACCATGAACAACTTTTCTCATCATGTCT

Reverse complement sequence

AGACATGATGAGAAAAGTTGTTCATGGTAGTCCAAACCGCAACAATGGTAAATTTATCCGGTCCAAATTGAAAAGATAGATTTAGGGGGGGGTCCAGAGT[A/G]
AAACTTGGGTAATAAAAGCTGGACCAAAGTGTAATTTACTAAAAAATGAATCTCATCATTTGTTTTATGTCTGATAAGTATTGGAAAAACAAATAAAGCA

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	85.80%	14.00%	0.28%	0.00%	NA
All Indica	2759	94.10%	5.90%	0.04%	0.00%	NA
All Japonica	1512	79.80%	19.40%	0.79%	0.00%	NA
Aus	269	47.60%	52.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	88.40%	11.60%	0.00%	0.00%	NA
Indica III	913	96.60%	3.30%	0.11%	0.00%	NA
Indica Intermediate	786	90.20%	9.80%	0.00%	0.00%	NA
Temperate Japonica	767	89.20%	9.50%	1.30%	0.00%	NA
Tropical Japonica	504	72.20%	27.80%	0.00%	0.00%	NA
Japonica Intermediate	241	66.00%	33.20%	0.83%	0.00%	NA
VI/Aromatic	96	51.00%	49.00%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	0.00%	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
vg1124963993	T -> C	LOC_Os11g41600-LOC_Os11g41610	intergenic_region ; MODIFIER	silent_mutation	Average:48.106; most accessible tissue: Callus, score: 77.215	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124963993	2.56E-13	NA	mr1238	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
vg1124963993	1.08E-08	NA	mr1309	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
vg1124963993	5.89E-10	NA	mr1484	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
vg1124963993	3.41E-06	NA	mr1566	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
vg1124963993	NA	1.77E-07	mr1723	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
vg1124963993	NA	2.72E-06	mr1729	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
vg1124963993	3.10E-10	NA	mr1841	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
vg1124963993	1.96E-07	NA	mr1900	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
vg1124963993	NA	8.75E-06	mr1906	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
vg1124963993	1.83E-06	5.64E-07	mr1925	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
vg1124963993	1.76E-06	NA	mr1945	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
vg1124963993	NA	7.75E-06	mr1170_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
vg1124963993	9.36E-10	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
vg1124963993	6.68E-08	NA	mr1484_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
vg1124963993	5.85E-06	NA	mr1609_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
vg1124963993	3.47E-11	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
vg1124963993	1.43E-09	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
vg1124963993	8.45E-06	2.09E-07	mr1925_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
vg1124963993	8.70E-07	NA	mr1945_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