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Detailed information for vg1125238334:

Variant ID: vg1125238334 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25238334
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.14, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCTGTACAATCCTCTGCTTTCAAATTCCTCCTGACCCCATTGCTTCGCCTTCATGGTCTCCAGCAGCAGCTGCTTGGTACACGCCGAGATGGGGATGG[G/A]
CAGGCCCGAGTAAGCCAACCTGTTCCACCAGTCCTCGACTCCCATCCACCTCGCAATCTTGCTGCATCGGCTGGCCCTGCTGTGCACGCACAACTGAATC

Reverse complement sequence

GATTCAGTTGTGCGTGCACAGCAGGGCCAGCCGATGCAGCAAGATTGCGAGGTGGATGGGAGTCGAGGACTGGTGGAACAGGTTGGCTTACTCGGGCCTG[C/T]
CCATCCCCATCTCGGCGTGTACCAAGCAGCTGCTGCTGGAGACCATGAAGGCGAAGCAATGGGGTCAGGAGGAATTTGAAAGCAGAGGATTGTACAGGGA

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	42.90%	25.40%	0.97%	30.66%	NA
All Indica	2759	27.70%	27.90%	1.38%	42.99%	NA
All Japonica	1512	66.00%	21.20%	0.13%	12.70%	NA
Aus	269	45.70%	34.20%	1.49%	18.59%	NA
Indica I	595	38.20%	2.70%	1.85%	57.31%	NA
Indica II	465	59.80%	34.00%	0.86%	5.38%	NA
Indica III	913	7.30%	38.70%	1.20%	52.79%	NA
Indica Intermediate	786	24.40%	31.00%	1.53%	43.00%	NA
Temperate Japonica	767	94.00%	3.40%	0.26%	2.35%	NA
Tropical Japonica	504	20.40%	51.00%	0.00%	28.57%	NA
Japonica Intermediate	241	72.20%	15.40%	0.00%	12.45%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	56.70%	18.90%	1.11%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125238334	G -> A	LOC_Os11g41970.1	upstream_gene_variant ; 3143.0bp to feature; MODIFIER	silent_mutation	Average:12.349; most accessible tissue: Callus, score: 64.526	N	N	N	N
vg1125238334	G -> A	LOC_Os11g41970-LOC_Os11g41990	intergenic_region ; MODIFIER	silent_mutation	Average:12.349; most accessible tissue: Callus, score: 64.526	N	N	N	N
vg1125238334	G -> DEL	N	N	silent_mutation	Average:12.349; most accessible tissue: Callus, score: 64.526	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125238334	9.34E-08	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
vg1125238334	5.03E-06	1.99E-06	mr1238	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
vg1125238334	3.30E-06	NA	mr1309	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
vg1125238334	NA	2.85E-06	mr1309	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
vg1125238334	1.45E-09	NA	mr1484	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
vg1125238334	2.58E-06	NA	mr1484	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
vg1125238334	7.34E-06	1.44E-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
vg1125238334	NA	2.61E-08	mr1723	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
vg1125238334	1.59E-06	NA	mr1841	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
vg1125238334	1.15E-06	NA	mr1925	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
vg1125238334	3.85E-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
vg1125238334	NA	1.97E-06	mr1609_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
vg1125238334	NA	1.02E-06	mr1723_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
vg1125238334	2.58E-06	NA	mr1841_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
vg1125238334	4.69E-06	NA	mr1900_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
vg1125238334	NA	1.65E-06	mr1900_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