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Detailed information for vg0714349436:

Variant ID: vg0714349436 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14349436
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGATTCTTGCTAGAGAGATCATTTGGAAAAACTCCAAATTGTTATTCCACTCAATTCCTAGGTATTGCCAACACCTGATGCTGAAAGGGCATAAAAAGAA[G/A]
AGGTGCAGTCTTGTCTCTCTGCAGTTCGCATTGCACAAAACACATGTGAGATCATCTTCTTTGGTACAATGTCTTCTATCCAGCATATCTCTTGTATTAA

Reverse complement sequence

TTAATACAAGAGATATGCTGGATAGAAGACATTGTACCAAAGAAGATGATCTCACATGTGTTTTGTGCAATGCGAACTGCAGAGAGACAAGACTGCACCT[C/T]
TTCTTTTTATGCCCTTTCAGCATCAGGTGTTGGCAATACCTAGGAATTGAGTGGAATAACAATTTGGAGTTTTTCCAAATGATCTCTCTAGCAAGAATCA

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	96.60%	0.10%	0.74%	2.58%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.04%	NA
All Japonica	1512	89.70%	0.10%	2.25%	7.94%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	90.00%	0.00%	1.43%	8.60%	NA
Tropical Japonica	504	96.80%	0.00%	1.39%	1.79%	NA
Japonica Intermediate	241	74.30%	0.40%	6.64%	18.67%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	100.00%	0.00%	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
vg0714349436	G -> DEL	N	N	silent_mutation	Average:12.074; most accessible tissue: Callus, score: 27.355	N	N	N	N
vg0714349436	G -> A	LOC_Os07g25110.1	upstream_gene_variant ; 3215.0bp to feature; MODIFIER	silent_mutation	Average:12.074; most accessible tissue: Callus, score: 27.355	N	N	N	N
vg0714349436	G -> A	LOC_Os07g25130.1	upstream_gene_variant ; 4406.0bp to feature; MODIFIER	silent_mutation	Average:12.074; most accessible tissue: Callus, score: 27.355	N	N	N	N
vg0714349436	G -> A	LOC_Os07g25120.1	intron_variant ; MODIFIER	silent_mutation	Average:12.074; most accessible tissue: Callus, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714349436	2.54E-06	NA	mr1950_2	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