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Detailed information for vg0125184019:

Variant ID: vg0125184019 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 25184019
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATGAGACTGTTCTCTGTATAGTTATAACCAGCTATCTCAATCTTATATCTAGTTACTATTAGTATACTCAAAAGTGTATGTATTTTTTTTCTTCTTATG[G/A]
AATTTTCTCTTAGATTACTCAGACGATTTACGATCCGATTACACCATTGTGTTTATAACAATTAAATCTTTATAACAAGATCTCACATGACTATATTTTT

Reverse complement sequence

AAAAATATAGTCATGTGAGATCTTGTTATAAAGATTTAATTGTTATAAACACAATGGTGTAATCGGATCGTAAATCGTCTGAGTAATCTAAGAGAAAATT[C/T]
CATAAGAAGAAAAAAAATACATACACTTTTGAGTATACTAATAGTAACTAGATATAAGATTGAGATAGCTGGTTATAACTATACAGAGAACAGTCTCATC

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	93.70%	4.90%	1.02%	0.32%	NA
All Indica	2759	92.00%	7.20%	0.83%	0.04%	NA
All Japonica	1512	98.80%	0.30%	0.86%	0.07%	NA
Aus	269	85.10%	10.40%	4.46%	0.00%	NA
Indica I	595	75.50%	23.50%	1.01%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	95.80%	3.10%	1.10%	0.00%	NA
Indica Intermediate	786	95.20%	3.80%	0.89%	0.13%	NA
Temperate Japonica	767	97.90%	0.50%	1.56%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	95.60%	3.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0125184019	G -> A	LOC_Os01g43940.1	upstream_gene_variant ; 3231.0bp to feature; MODIFIER	silent_mutation	Average:74.977; most accessible tissue: Callus, score: 97.804	N	N	N	N
vg0125184019	G -> A	LOC_Os01g43930-LOC_Os01g43940	intergenic_region ; MODIFIER	silent_mutation	Average:74.977; most accessible tissue: Callus, score: 97.804	N	N	N	N
vg0125184019	G -> DEL	N	N	silent_mutation	Average:74.977; most accessible tissue: Callus, score: 97.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0125184019	4.00E-06	5.27E-07	mr1817	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