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Detailed information for vg0711107694:

Variant ID: vg0711107694 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11107694
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAAGTCTGTTCGTTGTAAATGGATCTTCAAGAGAAAGGAGGGCTTATCTCCTAGTGAGCCTCTGAGGTTTAAGGCAAGGTTAGTAGCAAAAGGTTTCAG[T/A]
CAAATTGCTGGTGTTGATTATAATGATGTGTTCTCTCCAATTGTAAAGCATAGTTCCATTCGCACATTCTTCAGTATTGTTGCTATGCATGATCTTGAGC

Reverse complement sequence

GCTCAAGATCATGCATAGCAACAATACTGAAGAATGTGCGAATGGAACTATGCTTTACAATTGGAGAGAACACATCATTATAATCAACACCAGCAATTTG[A/T]
CTGAAACCTTTTGCTACTAACCTTGCCTTAAACCTCAGAGGCTCACTAGGAGATAAGCCCTCCTTTCTCTTGAAGATCCATTTACAACGAACAGACTTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.70%	32.00%	0.89%	15.49%	NA
All Indica	2759	79.50%	6.30%	1.30%	12.94%	NA
All Japonica	1512	1.90%	79.20%	0.20%	18.78%	NA
Aus	269	62.10%	33.10%	0.00%	4.83%	NA
Indica I	595	66.10%	1.70%	1.18%	31.09%	NA
Indica II	465	86.50%	8.20%	0.22%	5.16%	NA
Indica III	913	91.90%	5.80%	1.86%	0.44%	NA
Indica Intermediate	786	71.10%	9.20%	1.40%	18.32%	NA
Temperate Japonica	767	1.80%	66.20%	0.39%	31.55%	NA
Tropical Japonica	504	0.80%	98.60%	0.00%	0.60%	NA
Japonica Intermediate	241	4.10%	79.70%	0.00%	16.18%	NA
VI/Aromatic	96	16.70%	7.30%	2.08%	73.96%	NA
Intermediate	90	41.10%	50.00%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711107694	T -> DEL	N	N	silent_mutation	Average:14.515; most accessible tissue: Callus, score: 46.048	N	N	N	N
vg0711107694	T -> A	LOC_Os07g18770.1	upstream_gene_variant ; 3487.0bp to feature; MODIFIER	silent_mutation	Average:14.515; most accessible tissue: Callus, score: 46.048	N	N	N	N
vg0711107694	T -> A	LOC_Os07g18780.1	upstream_gene_variant ; 290.0bp to feature; MODIFIER	silent_mutation	Average:14.515; most accessible tissue: Callus, score: 46.048	N	N	N	N
vg0711107694	T -> A	LOC_Os07g18770-LOC_Os07g18780	intergenic_region ; MODIFIER	silent_mutation	Average:14.515; most accessible tissue: Callus, score: 46.048	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711107694	NA	9.49E-06	mr1106	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
vg0711107694	3.51E-06	3.51E-06	mr1370	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