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Detailed information for vg1125125737:

Variant ID: vg1125125737 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25125737
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAATAGTTAAGTGACTCACCATCTCAAAATCTAGCTCTATAGAACCAATTTTTTTTAAAAAAAAAGAGTAAAGTGTACGGGCACTCCTTAAACTTGTA[G/C]
GGGTATGCCATCTAGATCCCTAAACTCTCAAAATGCATATTTAAGTCCTAAAATTTGTCATAGTGTGTCATCTAGATCCCAAATCGCCACAACCCCTTCA

Reverse complement sequence

TGAAGGGGTTGTGGCGATTTGGGATCTAGATGACACACTATGACAAATTTTAGGACTTAAATATGCATTTTGAGAGTTTAGGGATCTAGATGGCATACCC[C/G]
TACAAGTTTAAGGAGTGCCCGTACACTTTACTCTTTTTTTTTAAAAAAAATTGGTTCTATAGAGCTAGATTTTGAGATGGTGAGTCACTTAACTATTTCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.40%	15.40%	0.13%	0.00%	NA
All Indica	2759	77.00%	22.80%	0.18%	0.00%	NA
All Japonica	1512	99.00%	1.00%	0.00%	0.00%	NA
Aus	269	72.50%	27.10%	0.37%	0.00%	NA
Indica I	595	64.40%	35.10%	0.50%	0.00%	NA
Indica II	465	79.10%	20.60%	0.22%	0.00%	NA
Indica III	913	79.10%	20.90%	0.00%	0.00%	NA
Indica Intermediate	786	82.80%	17.00%	0.13%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	0.00%	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
vg1125125737	G -> C	LOC_Os11g41800-LOC_Os11g41820	intergenic_region ; MODIFIER	silent_mutation	Average:45.828; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125125737	NA	5.23E-14	mr1191	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
vg1125125737	5.09E-06	3.44E-10	mr1191	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
vg1125125737	NA	9.34E-06	mr1530	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
vg1125125737	NA	1.59E-14	mr1644	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
vg1125125737	NA	1.35E-10	mr1644	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
vg1125125737	NA	8.45E-07	mr1745	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
vg1125125737	1.49E-07	1.03E-26	mr1191_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
vg1125125737	1.88E-07	9.56E-19	mr1191_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
vg1125125737	NA	9.80E-07	mr1530_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
vg1125125737	NA	1.45E-07	mr1662_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
vg1125125737	NA	1.48E-08	mr1662_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
vg1125125737	2.42E-07	7.25E-13	mr1745_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