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Detailed information for vg1120863964:

Variant ID: vg1120863964 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20863964
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.02, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

AATATATCTCAATCGGGCCCTAAGTTAAGCCCGTCACCGCTAGCTTTGACCCAGACGACCAGTCAAACTATAGCCCGTCACAGATGACCTATCTCTATCG[G/A]
GCGACAACTAGCGCCCGTCACAGATGACCCTTATCTGTGACGTGATGACCCTTATCTGTGACGGGCATCACGTCACAGATAAGGGTCATCTGTGACGGGC

Reverse complement sequence

GCCCGTCACAGATGACCCTTATCTGTGACGTGATGCCCGTCACAGATAAGGGTCATCACGTCACAGATAAGGGTCATCTGTGACGGGCGCTAGTTGTCGC[C/T]
CGATAGAGATAGGTCATCTGTGACGGGCTATAGTTTGACTGGTCGTCTGGGTCAAAGCTAGCGGTGACGGGCTTAACTTAGGGCCCGATTGAGATATATT

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	91.00%	1.60%	6.73%	0.72%	NA
All Indica	2759	86.10%	2.70%	10.00%	1.23%	NA
All Japonica	1512	98.10%	0.00%	1.85%	0.00%	NA
Aus	269	95.90%	0.00%	4.09%	0.00%	NA
Indica I	595	79.70%	4.70%	12.10%	3.53%	NA
Indica II	465	76.60%	5.60%	15.70%	2.15%	NA
Indica III	913	95.10%	0.30%	4.60%	0.00%	NA
Indica Intermediate	786	86.10%	2.20%	11.32%	0.38%	NA
Temperate Japonica	767	97.50%	0.00%	2.48%	0.00%	NA
Tropical Japonica	504	98.20%	0.00%	1.79%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	1.10%	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
vg1120863964	G -> A	LOC_Os11g35570.1	upstream_gene_variant ; 4695.0bp to feature; MODIFIER	silent_mutation	Average:36.352; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1120863964	G -> A	LOC_Os11g35580.1	upstream_gene_variant ; 1103.0bp to feature; MODIFIER	silent_mutation	Average:36.352; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1120863964	G -> A	LOC_Os11g35590.1	downstream_gene_variant ; 2856.0bp to feature; MODIFIER	silent_mutation	Average:36.352; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1120863964	G -> A	LOC_Os11g35580-LOC_Os11g35590	intergenic_region ; MODIFIER	silent_mutation	Average:36.352; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N
vg1120863964	G -> DEL	N	N	silent_mutation	Average:36.352; most accessible tissue: Zhenshan97 root, score: 54.262	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120863964	NA	4.63E-06	mr1325	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
vg1120863964	NA	1.64E-10	mr1581	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
vg1120863964	4.98E-06	4.98E-06	mr1581	Ind_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
vg1120863964	NA	3.38E-07	mr1038_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
vg1120863964	NA	2.52E-07	mr1038_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
vg1120863964	NA	2.44E-06	mr1389_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