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Detailed information for vg1103689189:

Variant ID: vg1103689189 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 3689189
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATTTATGCGGGTCCCATCTATATGGATCACTTTACCATATACATTGGTGATGCCCTTAGAGATTTGCTCAAGTCAAAAAAAAAGTATCTCAAGGTGC[C/T]
GGTACCTCATGGTACCAAATCGTTTATGATCATTGAAAAAAAAAACCTAAAGTACCCAAGCAATTGTACAATTAAGCACAATCCGACTGTTAAGCAGTAA

Reverse complement sequence

TTACTGCTTAACAGTCGGATTGTGCTTAATTGTACAATTGCTTGGGTACTTTAGGTTTTTTTTTTCAATGATCATAAACGATTTGGTACCATGAGGTACC[G/A]
GCACCTTGAGATACTTTTTTTTTGACTTGAGCAAATCTCTAAGGGCATCACCAATGTATATGGTAAAGTGATCCATATAGATGGGACCCGCATAAATAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	4.00%	1.04%	0.00%	NA
All Indica	2759	99.50%	0.20%	0.33%	0.00%	NA
All Japonica	1512	85.40%	12.00%	2.58%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.67%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.60%	0.51%	0.00%	NA
Temperate Japonica	767	90.90%	5.70%	3.39%	0.00%	NA
Tropical Japonica	504	83.90%	15.70%	0.40%	0.00%	NA
Japonica Intermediate	241	71.40%	24.10%	4.56%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg1103689189	C -> T	LOC_Os11g07320.1	upstream_gene_variant ; 1537.0bp to feature; MODIFIER	silent_mutation	Average:47.641; most accessible tissue: Callus, score: 80.023	N	N	N	N
vg1103689189	C -> T	LOC_Os11g07330.1	downstream_gene_variant ; 147.0bp to feature; MODIFIER	silent_mutation	Average:47.641; most accessible tissue: Callus, score: 80.023	N	N	N	N
vg1103689189	C -> T	LOC_Os11g07320-LOC_Os11g07330	intergenic_region ; MODIFIER	silent_mutation	Average:47.641; most accessible tissue: Callus, score: 80.023	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1103689189	NA	7.44E-06	mr1352	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
vg1103689189	1.39E-06	9.58E-09	mr1790	Jap_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