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Detailed information for vg1125239418:

Variant ID: vg1125239418 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25239418
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGCAGCAGCAGGAACGGTGCCCAGAGTGCCAACAGCTCATGCTCTGGTGACCTGCTGGTAACAGAGAGGTGGCCAAGCACGTAGATCGCTGTCCCGTC[G/A]
GCCAGCATGTATGCGGACCATATAAAGGCCCTTAGCACGCCAGAGTCAATGTACCGGCGGAATTCTGCCAAGATGAGGAGTGTGACTTGGACCATGAGGC

Reverse complement sequence

GCCTCATGGTCCAAGTCACACTCCTCATCTTGGCAGAATTCCGCCGGTACATTGACTCTGGCGTGCTAAGGGCCTTTATATGGTCCGCATACATGCTGGC[C/T]
GACGGGACAGCGATCTACGTGCTTGGCCACCTCTCTGTTACCAGCAGGTCACCAGAGCATGAGCTGTTGGCACTCTGGGCACCGTTCCTGCTGCTGCACC

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	61.90%	7.40%	2.31%	28.37%	NA
All Indica	2759	55.40%	1.20%	3.37%	40.09%	NA
All Japonica	1512	68.70%	19.20%	0.60%	11.51%	NA
Aus	269	74.70%	7.10%	1.49%	16.73%	NA
Indica I	595	40.00%	1.30%	4.87%	53.78%	NA
Indica II	465	94.40%	0.20%	0.43%	4.95%	NA
Indica III	913	45.70%	1.50%	3.94%	48.85%	NA
Indica Intermediate	786	55.20%	1.10%	3.31%	40.33%	NA
Temperate Japonica	767	93.60%	4.00%	0.13%	2.22%	NA
Tropical Japonica	504	26.80%	46.00%	1.39%	25.79%	NA
Japonica Intermediate	241	76.80%	11.60%	0.41%	11.20%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	4.40%	3.33%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125239418	G -> A	LOC_Os11g41970.1	upstream_gene_variant ; 4227.0bp to feature; MODIFIER	silent_mutation	Average:15.283; most accessible tissue: Callus, score: 72.039	N	N	N	N
vg1125239418	G -> A	LOC_Os11g41970-LOC_Os11g41990	intergenic_region ; MODIFIER	silent_mutation	Average:15.283; most accessible tissue: Callus, score: 72.039	N	N	N	N
vg1125239418	G -> DEL	N	N	silent_mutation	Average:15.283; most accessible tissue: Callus, score: 72.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125239418	2.69E-07	NA	mr1238	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
vg1125239418	NA	4.49E-08	mr1248	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
vg1125239418	NA	3.63E-09	mr1249	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
vg1125239418	NA	4.46E-06	mr1328	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
vg1125239418	1.31E-06	NA	mr1484	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
vg1125239418	2.09E-07	NA	mr1662	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
vg1125239418	NA	1.38E-07	mr1662	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
vg1125239418	3.25E-06	NA	mr1238_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
vg1125239418	5.53E-06	NA	mr1484_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
vg1125239418	1.00E-07	NA	mr1662_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
vg1125239418	4.48E-07	3.17E-09	mr1662_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