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Detailed information for vg1121340366:

Variant ID: vg1121340366 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21340366
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GCCTCTGCGGATGCCAAGATCTTCATCGCCATGATCGTCGCCGGCTCCGCCTGTAGAAAATACGGAAGCGTTGTCACCTCTCTCGAGGCCGCGTACGTGT[G/A]
TTAATATGAGTTGGGAACAGCCCCCAACGTGGCTTACAATAGATGAGATCAATCTCAGTTGATTCGGATAGAAGAAAGAAACAAACTCTGAAACAAACTA

Reverse complement sequence

TAGTTTGTTTCAGAGTTTGTTTCTTTCTTCTATCCGAATCAACTGAGATTGATCTCATCTATTGTAAGCCACGTTGGGGGCTGTTCCCAACTCATATTAA[C/T]
ACACGTACGCGGCCTCGAGAGAGGTGACAACGCTTCCGTATTTTCTACAGGCGGAGCCGGCGACGATCATGGCGATGAAGATCTTGGCATCCGCAGAGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.30%	23.80%	0.40%	2.50%	NA
All Indica	2759	60.60%	38.60%	0.22%	0.58%	NA
All Japonica	1512	95.90%	3.20%	0.00%	0.93%	NA
Aus	269	62.80%	0.70%	4.46%	31.97%	NA
Indica I	595	69.60%	30.30%	0.00%	0.17%	NA
Indica II	465	45.40%	52.00%	0.43%	2.15%	NA
Indica III	913	63.40%	36.30%	0.11%	0.22%	NA
Indica Intermediate	786	59.70%	39.60%	0.38%	0.38%	NA
Temperate Japonica	767	95.00%	3.30%	0.00%	1.69%	NA
Tropical Japonica	504	96.00%	3.80%	0.00%	0.20%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	13.30%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121340366	G -> A	LOC_Os11g36240.1	downstream_gene_variant ; 2387.0bp to feature; MODIFIER	silent_mutation	Average:55.248; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N
vg1121340366	G -> A	LOC_Os11g36240-LOC_Os11g36260	intergenic_region ; MODIFIER	silent_mutation	Average:55.248; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N
vg1121340366	G -> DEL	N	N	silent_mutation	Average:55.248; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121340366	NA	1.71E-08	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
vg1121340366	NA	7.14E-06	mr1517_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
vg1121340366	4.47E-06	4.47E-06	mr1527_2	Jap_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