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Detailed information for vg0714095299:

Variant ID: vg0714095299 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14095299
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGGATCAACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTGCCTTGCTGGCCTTGGAATTCCTCAAATTCTTTTCCTGCAAATTCGGACTCTCCG[A/G]
GAACGTCGGAATCTAAAGAGAAAAGAACAAAATCACCAAAACAGCACATAAACAAGCATGAACAGTACATGTGGATATTTTTAACATGTAGATCTCAATT

Reverse complement sequence

AATTGAGATCTACATGTTAAAAATATCCACATGTACTGTTCATGCTTGTTTATGTGCTGTTTTGGTGATTTTGTTCTTTTCTCTTTAGATTCCGACGTTC[T/C]
CGGAGAGTCCGAATTTGCAGGAAAAGAATTTGAGGAATTCCAAGGCCAGCAAGGCAAGTCACACAGATCCCAAACAACCCTTTGAGCATGTTGATCCCGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.10%	9.50%	42.81%	5.50%	NA
All Indica	2759	19.20%	13.30%	60.96%	6.52%	NA
All Japonica	1512	85.40%	3.20%	7.14%	4.30%	NA
Aus	269	14.90%	12.30%	69.89%	2.97%	NA
Indica I	595	37.30%	11.90%	43.87%	6.89%	NA
Indica II	465	18.10%	4.70%	64.09%	13.12%	NA
Indica III	913	5.70%	20.00%	70.87%	3.40%	NA
Indica Intermediate	786	22.00%	11.50%	60.56%	5.98%	NA
Temperate Japonica	767	86.70%	1.40%	7.30%	4.56%	NA
Tropical Japonica	504	93.50%	0.80%	5.36%	0.40%	NA
Japonica Intermediate	241	64.30%	13.70%	10.37%	11.62%	NA
VI/Aromatic	96	81.20%	1.00%	16.67%	1.04%	NA
Intermediate	90	57.80%	3.30%	32.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714095299	A -> DEL	N	N	silent_mutation	Average:7.342; most accessible tissue: Callus, score: 19.034	N	N	N	N
vg0714095299	A -> G	LOC_Os07g24790.1	upstream_gene_variant ; 844.0bp to feature; MODIFIER	silent_mutation	Average:7.342; most accessible tissue: Callus, score: 19.034	N	N	N	N
vg0714095299	A -> G	LOC_Os07g24800.1	upstream_gene_variant ; 643.0bp to feature; MODIFIER	silent_mutation	Average:7.342; most accessible tissue: Callus, score: 19.034	N	N	N	N
vg0714095299	A -> G	LOC_Os07g24790-LOC_Os07g24800	intergenic_region ; MODIFIER	silent_mutation	Average:7.342; most accessible tissue: Callus, score: 19.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714095299	7.43E-08	7.43E-08	mr1300	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