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Detailed information for vg0606310477:

Variant ID: vg0606310477 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6310477
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGACTACAACAACGGAGGCAATTCTGCCTCACCATCCAGCGGAGGGCCATTCTCGGGGTATAATCTTCTCCTCCTGCTACTGCTGTTAGCGCTATTCTT[G/A]
TTCCCATTGTTAGCGCTATACTGTGTGCGCTGTGTTCATGTTCCTGTTTCTGACATTCATGATGCGCATAGTATGCTACTGGTTATGTTAAGATCACTCT

Reverse complement sequence

AGAGTGATCTTAACATAACCAGTAGCATACTATGCGCATCATGAATGTCAGAAACAGGAACATGAACACAGCGCACACAGTATAGCGCTAACAATGGGAA[C/T]
AAGAATAGCGCTAACAGCAGTAGCAGGAGGAGAAGATTATACCCCGAGAATGGCCCTCCGCTGGATGGTGAGGCAGAATTGCCTCCGTTGTTGTAGTCGT

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	87.10%	0.30%	3.11%	9.59%	NA
All Indica	2759	94.10%	0.40%	2.54%	2.97%	NA
All Japonica	1512	79.90%	0.00%	3.04%	17.06%	NA
Aus	269	82.20%	0.00%	0.37%	17.47%	NA
Indica I	595	94.60%	0.50%	3.19%	1.68%	NA
Indica II	465	89.70%	0.90%	3.87%	5.59%	NA
Indica III	913	96.60%	0.20%	1.20%	1.97%	NA
Indica Intermediate	786	93.30%	0.40%	2.80%	3.56%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	48.20%	0.00%	8.53%	43.25%	NA
Japonica Intermediate	241	84.60%	0.00%	1.24%	14.11%	NA
VI/Aromatic	96	17.70%	0.00%	25.00%	57.29%	NA
Intermediate	90	81.10%	0.00%	6.67%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0606310477	G -> A	LOC_Os06g11860.1	upstream_gene_variant ; 3816.0bp to feature; MODIFIER	silent_mutation	Average:32.176; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0606310477	G -> A	LOC_Os06g11870.1	upstream_gene_variant ; 196.0bp to feature; MODIFIER	silent_mutation	Average:32.176; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0606310477	G -> A	LOC_Os06g11870-LOC_Os06g11880	intergenic_region ; MODIFIER	silent_mutation	Average:32.176; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0606310477	G -> DEL	N	N	silent_mutation	Average:32.176; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0606310477	4.04E-07	2.49E-07	mr1379_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
vg0606310477	NA	2.03E-07	mr1613_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251