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Detailed information for vg0407756297:

Variant ID: vg0407756297 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7756297
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGACATGTGGGGTCCGCATGTCAACAGCGCAGCCTTCCTGTCTTTTCCAGGCTAGCGCTTACACATGTTTTATAGTTGCAAAGCCTAATTATAATAATCC[A/G]
CAAATCTCCATATAACAGCATTAAACTTCGGATGATCATATCTTGGTCATACGGACTCTGAATCGACCCGTTCAAGTCTCCTAATGTTGGTTATAACCTA

Reverse complement sequence

TAGGTTATAACCAACATTAGGAGACTTGAACGGGTCGATTCAGAGTCCGTATGACCAAGATATGATCATCCGAAGTTTAATGCTGTTATATGGAGATTTG[T/C]
GGATTATTATAATTAGGCTTTGCAACTATAAAACATGTGTAAGCGCTAGCCTGGAAAAGACAGGAAGGCTGCGCTGTTGACATGCGGACCCCACATGTCA

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	51.80%	2.10%	8.91%	37.18%	NA
All Indica	2759	29.50%	0.80%	10.44%	59.26%	NA
All Japonica	1512	97.00%	0.70%	1.65%	0.60%	NA
Aus	269	30.90%	2.20%	35.69%	31.23%	NA
Indica I	595	50.60%	0.50%	5.71%	43.19%	NA
Indica II	465	35.70%	0.00%	7.10%	57.20%	NA
Indica III	913	8.20%	1.80%	16.21%	73.82%	NA
Indica Intermediate	786	34.50%	0.50%	9.29%	55.73%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	94.00%	1.40%	4.17%	0.40%	NA
Japonica Intermediate	241	95.40%	1.70%	0.83%	2.07%	NA
VI/Aromatic	96	29.20%	58.30%	8.33%	4.17%	NA
Intermediate	90	63.30%	4.40%	4.44%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407756297	A -> DEL	N	N	silent_mutation	Average:10.474; most accessible tissue: Callus, score: 28.168	N	N	N	N
vg0407756297	A -> G	LOC_Os04g13890.1	upstream_gene_variant ; 828.0bp to feature; MODIFIER	silent_mutation	Average:10.474; most accessible tissue: Callus, score: 28.168	N	N	N	N
vg0407756297	A -> G	LOC_Os04g13890-LOC_Os04g13900	intergenic_region ; MODIFIER	silent_mutation	Average:10.474; most accessible tissue: Callus, score: 28.168	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407756297	4.20E-06	1.15E-07	mr1558_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