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Detailed information for vg0617484074:

Variant ID: vg0617484074 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17484074
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGTGGTGAATAGCGCTCATAAACCACTCAAAAGGTGTAAACCACCCAAAATATATTGTGTTATGAGTTGTGCACTAATTAAACACAGTTTTCTATTCTA[A/G]
TAGCAACATGTTGTGTGTTTTCTGCCTAACATATTGATATGGTTGTGAAAGATATGTCCCAGGATCGAATTATTAAGCTAAGTATTTGCTAATGGATCCA

Reverse complement sequence

TGGATCCATTAGCAAATACTTAGCTTAATAATTCGATCCTGGGACATATCTTTCACAACCATATCAATATGTTAGGCAGAAAACACACAACATGTTGCTA[T/C]
TAGAATAGAAAACTGTGTTTAATTAGTGCACAACTCATAACACAATATATTTTGGGTGGTTTACACCTTTTGAGTGGTTTATGAGCGCTATTCACCACTC

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	53.30%	30.20%	1.44%	15.00%	NA
All Indica	2759	80.60%	2.20%	1.12%	16.06%	NA
All Japonica	1512	4.50%	86.00%	1.79%	7.74%	NA
Aus	269	64.30%	11.20%	1.86%	22.68%	NA
Indica I	595	88.60%	2.00%	0.84%	8.57%	NA
Indica II	465	89.00%	1.30%	0.22%	9.46%	NA
Indica III	913	74.80%	1.50%	1.42%	22.23%	NA
Indica Intermediate	786	76.20%	3.80%	1.53%	18.45%	NA
Temperate Japonica	767	0.90%	92.80%	3.26%	3.00%	NA
Tropical Japonica	504	10.90%	74.00%	0.20%	14.88%	NA
Japonica Intermediate	241	2.50%	89.20%	0.41%	7.88%	NA
VI/Aromatic	96	26.00%	4.20%	1.04%	68.75%	NA
Intermediate	90	35.60%	35.60%	4.44%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617484074	A -> G	LOC_Os06g30310.1	upstream_gene_variant ; 4758.0bp to feature; MODIFIER	silent_mutation	Average:18.985; most accessible tissue: Callus, score: 54.672	N	N	N	N
vg0617484074	A -> G	LOC_Os06g30290.1	downstream_gene_variant ; 1859.0bp to feature; MODIFIER	silent_mutation	Average:18.985; most accessible tissue: Callus, score: 54.672	N	N	N	N
vg0617484074	A -> G	LOC_Os06g30300.1	downstream_gene_variant ; 3563.0bp to feature; MODIFIER	silent_mutation	Average:18.985; most accessible tissue: Callus, score: 54.672	N	N	N	N
vg0617484074	A -> G	LOC_Os06g30290-LOC_Os06g30300	intergenic_region ; MODIFIER	silent_mutation	Average:18.985; most accessible tissue: Callus, score: 54.672	N	N	N	N
vg0617484074	A -> DEL	N	N	silent_mutation	Average:18.985; most accessible tissue: Callus, score: 54.672	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617484074	3.83E-06	NA	mr1622_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