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Detailed information for vg1127682350:

Variant ID: vg1127682350 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27682350
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCTGCGATCAGGATCGGCAGAGTTCGAGTCGGACTAGGTAGCCGATTGAGCCGATTCCGATAATGTGACTCGGTATTCGTTATCGGGTTGAGTTAATGT[G/A]
CTTCATATGGATTGCCACGCACGGATTGAGTCCTGAGAAGGCAATTGTATCTATTAATTAGGATATTTTATGTAATTTTTTTAGAGATAAGTTTGGGCAA

Reverse complement sequence

TTGCCCAAACTTATCTCTAAAAAAATTACATAAAATATCCTAATTAATAGATACAATTGCCTTCTCAGGACTCAATCCGTGCGTGGCAATCCATATGAAG[C/T]
ACATTAACTCAACCCGATAACGAATACCGAGTCACATTATCGGAATCGGCTCAATCGGCTACCTAGTCCGACTCGAACTCTGCCGATCCTGATCGCAGCC

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	21.60%	0.10%	11.98%	66.27%	NA
All Indica	2759	20.40%	0.10%	16.93%	62.60%	NA
All Japonica	1512	26.60%	0.00%	1.85%	71.56%	NA
Aus	269	10.40%	1.10%	19.70%	68.77%	NA
Indica I	595	25.00%	0.00%	21.85%	53.11%	NA
Indica II	465	11.20%	0.00%	22.58%	66.24%	NA
Indica III	913	20.00%	0.20%	12.38%	67.36%	NA
Indica Intermediate	786	22.80%	0.00%	15.14%	62.09%	NA
Temperate Japonica	767	35.60%	0.00%	1.56%	62.84%	NA
Tropical Japonica	504	8.90%	0.00%	2.38%	88.69%	NA
Japonica Intermediate	241	34.90%	0.00%	1.66%	63.49%	NA
VI/Aromatic	96	8.30%	0.00%	11.46%	80.21%	NA
Intermediate	90	24.40%	0.00%	7.78%	67.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127682350	G -> A	LOC_Os11g45750.1	downstream_gene_variant ; 1403.0bp to feature; MODIFIER	silent_mutation	Average:12.917; most accessible tissue: Callus, score: 32.926	N	N	N	N
vg1127682350	G -> A	LOC_Os11g45750.2	downstream_gene_variant ; 1290.0bp to feature; MODIFIER	silent_mutation	Average:12.917; most accessible tissue: Callus, score: 32.926	N	N	N	N
vg1127682350	G -> A	LOC_Os11g45740-LOC_Os11g45750	intergenic_region ; MODIFIER	silent_mutation	Average:12.917; most accessible tissue: Callus, score: 32.926	N	N	N	N
vg1127682350	G -> DEL	N	N	silent_mutation	Average:12.917; most accessible tissue: Callus, score: 32.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127682350	NA	5.76E-06	mr1212	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
vg1127682350	NA	6.68E-08	mr1559	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
vg1127682350	NA	3.00E-06	mr1806_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