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Detailed information for vg1114292062:

Variant ID: vg1114292062 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14292062
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGGGCCATGTAATGGGGGGATCCCAAGTAAAAATTCTCAAATTAATACACTTTACTTCTGTTTCAACCACTATTGAGTAACCACGTCTTTCGACGTAT[G/A]
CGGTTGTCGTTTCGACAACAGCTAGCGCCGACCGTGGGGAACTCCTAGCAAAACCACTGAGAGCGAATGCCACCGAAGAAGGTCGTGAAGGAGAAGGTTA

Reverse complement sequence

TAACCTTCTCCTTCACGACCTTCTTCGGTGGCATTCGCTCTCAGTGGTTTTGCTAGGAGTTCCCCACGGTCGGCGCTAGCTGTTGTCGAAACGACAACCG[C/T]
ATACGTCGAAAGACGTGGTTACTCAATAGTGGTTGAAACAGAAGTAAAGTGTATTAATTTGAGAATTTTTACTTGGGATCCCCCCATTACATGGCCCTAT

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	88.30%	1.20%	4.25%	6.24%	NA
All Indica	2759	81.40%	2.00%	7.14%	9.42%	NA
All Japonica	1512	99.30%	0.00%	0.07%	0.66%	NA
Aus	269	95.50%	0.00%	0.00%	4.46%	NA
Indica I	595	85.40%	0.80%	5.38%	8.40%	NA
Indica II	465	64.10%	1.90%	9.89%	24.09%	NA
Indica III	913	88.20%	2.70%	6.68%	2.41%	NA
Indica Intermediate	786	80.80%	2.20%	7.38%	9.67%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	98.60%	0.00%	0.20%	1.19%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	0.00%	3.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114292062	G -> A	LOC_Os11g25060.1	downstream_gene_variant ; 1209.0bp to feature; MODIFIER	silent_mutation	Average:15.17; most accessible tissue: Callus, score: 18.513	N	N	N	N
vg1114292062	G -> A	LOC_Os11g25070.1	intron_variant ; MODIFIER	silent_mutation	Average:15.17; most accessible tissue: Callus, score: 18.513	N	N	N	N
vg1114292062	G -> DEL	N	N	silent_mutation	Average:15.17; most accessible tissue: Callus, score: 18.513	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114292062	2.08E-07	8.80E-10	mr1172_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
vg1114292062	8.12E-06	NA	mr1172_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