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Detailed information for vg0714953061:

Variant ID: vg0714953061 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14953061
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATTAGCTAATACTTAATTAATCACGCACTAAATGCTGCTCCGTTTTGCGTGCACCCTCACTCCCGAACGCAGCCTTAGGAGTATTTGTAGGAGTGTAG[A/G]
AATGCTATTACTCATACTCACAATCTATTTGTAGTTAACTATTATTTGATGTGGCTTGGTGGCACTCTCTATTTAACTATCATTTTGTTCATACATGCCC

Reverse complement sequence

GGGCATGTATGAACAAAATGATAGTTAAATAGAGAGTGCCACCAAGCCACATCAAATAATAGTTAACTACAAATAGATTGTGAGTATGAGTAATAGCATT[T/C]
CTACACTCCTACAAATACTCCTAAGGCTGCGTTCGGGAGTGAGGGTGCACGCAAAACGGAGCAGCATTTAGTGCGTGATTAATTAAGTATTAGCTAATTT

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	34.80%	3.00%	1.50%	60.69%	NA
All Indica	2759	4.90%	0.10%	2.36%	92.64%	NA
All Japonica	1512	93.20%	5.60%	0.00%	1.26%	NA
Aus	269	4.10%	5.20%	1.49%	89.22%	NA
Indica I	595	4.90%	0.00%	1.68%	93.45%	NA
Indica II	465	6.50%	0.00%	2.37%	91.18%	NA
Indica III	913	3.00%	0.10%	2.74%	94.19%	NA
Indica Intermediate	786	6.20%	0.30%	2.42%	91.09%	NA
Temperate Japonica	767	87.70%	10.60%	0.00%	1.69%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	44.80%	40.60%	0.00%	14.58%	NA
Intermediate	90	52.20%	2.20%	2.22%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714953061	A -> DEL	N	N	silent_mutation	Average:9.863; most accessible tissue: Callus, score: 36.48	N	N	N	N
vg0714953061	A -> G	LOC_Os07g26060-LOC_Os07g26070	intergenic_region ; MODIFIER	silent_mutation	Average:9.863; most accessible tissue: Callus, score: 36.48	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714953061	1.35E-06	1.40E-06	mr1553_2	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