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Detailed information for vg0413191246:

Variant ID: vg0413191246 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13191246
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATTGACTTTGAGGTGGAAAAATTTTGTATTTGCATCTCCCTCCTTGATGTGCATTACGCGGGAAGCTTGCCTCTTCCTTGCGCGTTCAAGCGTTGCCAG[G/A]
CCAAGTAGGCGGCGTTTAAGTCCTGCTCTCAGCCGGTGCTCTAGCGTTGTGAGCTCTCTTTGCTCCTATGCGGAGTCTAGCCGCTGGATGACGTCAAGCG

Reverse complement sequence

CGCTTGACGTCATCCAGCGGCTAGACTCCGCATAGGAGCAAAGAGAGCTCACAACGCTAGAGCACCGGCTGAGAGCAGGACTTAAACGCCGCCTACTTGG[C/T]
CTGGCAACGCTTGAACGCGCAAGGAAGAGGCAAGCTTCCCGCGTAATGCACATCAAGGAGGGAGATGCAAATACAAAATTTTTCCACCTCAAAGTCAATG

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	61.80%	10.50%	1.82%	25.84%	NA
All Indica	2759	45.30%	17.70%	2.72%	34.32%	NA
All Japonica	1512	97.80%	0.00%	0.07%	2.12%	NA
Aus	269	11.50%	3.00%	2.97%	82.53%	NA
Indica I	595	54.60%	2.40%	2.52%	40.50%	NA
Indica II	465	75.10%	1.50%	1.08%	22.37%	NA
Indica III	913	24.30%	39.10%	4.60%	31.98%	NA
Indica Intermediate	786	45.00%	13.90%	1.65%	39.44%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	94.20%	0.00%	0.41%	5.39%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	2.20%	2.22%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413191246	G -> DEL	N	N	silent_mutation	Average:7.865; most accessible tissue: Callus, score: 39.834	N	N	N	N
vg0413191246	G -> A	LOC_Os04g23190.1	upstream_gene_variant ; 46.0bp to feature; MODIFIER	silent_mutation	Average:7.865; most accessible tissue: Callus, score: 39.834	N	N	N	N
vg0413191246	G -> A	LOC_Os04g23200.1	downstream_gene_variant ; 1589.0bp to feature; MODIFIER	silent_mutation	Average:7.865; most accessible tissue: Callus, score: 39.834	N	N	N	N
vg0413191246	G -> A	LOC_Os04g23190-LOC_Os04g23200	intergenic_region ; MODIFIER	silent_mutation	Average:7.865; most accessible tissue: Callus, score: 39.834	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413191246	1.07E-06	2.08E-06	mr1916_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