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Detailed information for vg0714623737:

Variant ID: vg0714623737 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14623737
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTTCATCTTGGAACAATTTGATTAAATATCAGAATCATAACATATTTTAACTGTGCATATATATTTAAAATATCGACATGGTTTAACTGTCCAATTTTT[C/G]
TATTTATATGTTGTAAAATATATATAATATGTGCCTAGGGTATCATGAAATAGAAAGTGTACATATAGAGACTCTTAATGCCATTTATACATGACAAATA

Reverse complement sequence

TATTTGTCATGTATAAATGGCATTAAGAGTCTCTATATGTACACTTTCTATTTCATGATACCCTAGGCACATATTATATATATTTTACAACATATAAATA[G/C]
AAAAATTGGACAGTTAAACCATGTCGATATTTTAAATATATATGCACAGTTAAAATATGTTATGATTCTGATATTTAATCAAATTGTTCCAAGATGAACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	2.90%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.90%	9.10%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	83.10%	16.90%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0714623737	C -> G	LOC_Os07g25540.1	upstream_gene_variant ; 3236.0bp to feature; MODIFIER	silent_mutation	Average:31.102; most accessible tissue: Callus, score: 66.032	N	N	N	N
vg0714623737	C -> G	LOC_Os07g25540-LOC_Os07g25550	intergenic_region ; MODIFIER	silent_mutation	Average:31.102; most accessible tissue: Callus, score: 66.032	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714623737	NA	9.39E-06	mr1030_2	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
vg0714623737	3.69E-06	3.69E-06	mr1571_2	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