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Detailed information for vg1111092734:

Variant ID: vg1111092734 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11092734
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGTTATTCTGGTCATCATCAAATTCCCATCCATCCCGATAACCAAGGAAAAGACCATGTTCTCATATCCTTATGGAACATATGCTTACTGCGGAATGT[C/T]
ATTTGGGTTGTGTAATGCAGCTGCGTCATTCCAAAGGTGCATGTTGTCTATTTGCTCTGACATGATCAAGAAAATCATGGAAGTTTTCATGGACGACTTC

Reverse complement sequence

GAAGTCGTCCATGAAAACTTCCATGATTTTCTTGATCATGTCAGAGCAAATAGACAACATGCACCTTTGGAATGACGCAGCTGCATTACACAACCCAAAT[G/A]
ACATTCCGCAGTAAGCATATGTTCCATAAGGATATGAGAACATGGTCTTTTCCTTGGTTATCGGGATGGATGGGAATTTGATGATGACCAGAATAACCAT

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	91.50%	7.80%	0.76%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.00%	NA
All Japonica	1512	74.40%	23.50%	2.05%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	97.70%	1.70%	0.65%	0.00%	NA
Tropical Japonica	504	46.60%	50.20%	3.17%	0.00%	NA
Japonica Intermediate	241	58.50%	37.30%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	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
vg1111092734	C -> T	LOC_Os11g19330-LOC_Os11g19340	intergenic_region ; MODIFIER	silent_mutation	Average:35.115; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111092734	NA	7.00E-07	mr1248	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
vg1111092734	6.15E-06	NA	mr1745	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
vg1111092734	NA	3.43E-07	mr1180_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
vg1111092734	NA	4.32E-06	mr1194_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
vg1111092734	5.64E-07	NA	mr1241_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
vg1111092734	NA	2.90E-13	mr1241_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
vg1111092734	NA	6.30E-06	mr1246_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
vg1111092734	NA	1.45E-06	mr1966_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