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Detailed information for vg1121793608:

Variant ID: vg1121793608 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21793608
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.26, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ACCACTCCTCTAGGCTTGTCCAAGATCCGGGCACCACTCCATACGGTTTTAATCTATACCGTGATATCCCATACATCTTGGTGAAAAAAATTGATGTGCC[A/G]
GATTGGAGATCTGTTTGCAAAAATGGAACCTACATGTCGAGAGCATTCTATTTTTATATGATTTTAATTTTTGGTATGTAATTTTGCATTTGAGTCCCTG

Reverse complement sequence

CAGGGACTCAAATGCAAAATTACATACCAAAAATTAAAATCATATAAAAATAGAATGCTCTCGACATGTAGGTTCCATTTTTGCAAACAGATCTCCAATC[T/C]
GGCACATCAATTTTTTTCACCAAGATGTATGGGATATCACGGTATAGATTAAAACCGTATGGAGTGGTGCCCGGATCTTGGACAAGCCTAGAGGAGTGGT

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	58.60%	16.80%	0.55%	24.06%	NA
All Indica	2759	73.00%	0.90%	0.36%	25.81%	NA
All Japonica	1512	34.50%	46.20%	0.60%	18.72%	NA
Aus	269	56.50%	23.40%	1.12%	18.96%	NA
Indica I	595	77.10%	1.00%	0.34%	21.51%	NA
Indica II	465	70.80%	0.40%	0.43%	28.39%	NA
Indica III	913	71.60%	0.50%	0.33%	27.49%	NA
Indica Intermediate	786	72.60%	1.40%	0.38%	25.57%	NA
Temperate Japonica	767	22.80%	73.30%	0.13%	3.78%	NA
Tropical Japonica	504	46.20%	8.10%	1.19%	44.44%	NA
Japonica Intermediate	241	46.90%	39.80%	0.83%	12.45%	NA
VI/Aromatic	96	28.10%	0.00%	2.08%	69.79%	NA
Intermediate	90	61.10%	10.00%	2.22%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121793608	A -> DEL	N	N	silent_mutation	Average:22.083; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1121793608	A -> G	LOC_Os11g36950.1	upstream_gene_variant ; 3178.0bp to feature; MODIFIER	silent_mutation	Average:22.083; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1121793608	A -> G	LOC_Os11g36930.1	downstream_gene_variant ; 4581.0bp to feature; MODIFIER	silent_mutation	Average:22.083; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1121793608	A -> G	LOC_Os11g36940.1	downstream_gene_variant ; 2029.0bp to feature; MODIFIER	silent_mutation	Average:22.083; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1121793608	A -> G	LOC_Os11g36940-LOC_Os11g36950	intergenic_region ; MODIFIER	silent_mutation	Average:22.083; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121793608	NA	3.14E-06	mr1119_2	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
vg1121793608	NA	6.46E-06	mr1330_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