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Detailed information for vg1113597253:

Variant ID: vg1113597253 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13597253
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CCACCCGTTTCGAGAGGAGAGCAACTCCGTCTGCACAGTTCAGGACACACCTTGCTGCTACAACCCGATAGTGACCCGATTGTCACGATGGGCTGAGGCC[G/A]
TAGACGACTTTTACGAGGAGGCTCTGTTAGAGATCGACGACTAGCAGAGGCGTGTGGGAGAGTTAGAGATCGAGGTGACTGACCTCACAGTGCAGCAGCT

Reverse complement sequence

AGCTGCTGCACTGTGAGGTCAGTCACCTCGATCTCTAACTCTCCCACACGCCTCTGCTAGTCGTCGATCTCTAACAGAGCCTCCTCGTAAAAGTCGTCTA[C/T]
GGCCTCAGCCCATCGTGACAATCGGGTCACTATCGGGTTGTAGCAGCAAGGTGTGTCCTGAACTGTGCAGACGGAGTTGCTCTCCTCTCGAAACGGGTGG

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	97.40%	1.60%	1.02%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.14%	0.00%	NA
All Japonica	1512	92.30%	4.80%	2.84%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	88.90%	6.40%	4.69%	0.00%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	1.70%	2.90%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg1113597253	G -> A	LOC_Os11g24000.1	upstream_gene_variant ; 1232.0bp to feature; MODIFIER	silent_mutation	Average:39.715; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg1113597253	G -> A	LOC_Os11g23980.1	downstream_gene_variant ; 4190.0bp to feature; MODIFIER	silent_mutation	Average:39.715; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg1113597253	G -> A	LOC_Os11g23990.1	intron_variant ; MODIFIER	silent_mutation	Average:39.715; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113597253	NA	2.70E-06	mr1062	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
vg1113597253	1.33E-06	7.24E-09	mr1062_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