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Detailed information for vg0612517051:

Variant ID: vg0612517051 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 12517051
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAATTTAACCCCAATCCAGGGTCAAACGAAGATACTTGTTAGCCTAGCATCATGTGTATCTGTAGCCTTCCCTATTTTTGACAATCTCCTATTTCTTC[G/A]
TAGCACGTGTCTCCTTCCTATGTTCCGTCCCCTGTTACTGGATAAGTAGATTTTCTGTTTGAAGTGCCTAGAAGATCCAGCAAACGGAGGTTATCTCTCC

Reverse complement sequence

GGAGAGATAACCTCCGTTTGCTGGATCTTCTAGGCACTTCAAACAGAAAATCTACTTATCCAGTAACAGGGGACGGAACATAGGAAGGAGACACGTGCTA[C/T]
GAAGAAATAGGAGATTGTCAAAAATAGGGAAGGCTACAGATACACATGATGCTAGGCTAACAAGTATCTTCGTTTGACCCTGGATTGGGGTTAAATTTCC

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	66.80%	33.10%	0.15%	0.00%	NA
All Indica	2759	96.90%	2.90%	0.18%	0.00%	NA
All Japonica	1512	11.10%	88.90%	0.00%	0.00%	NA
Aus	269	83.60%	16.40%	0.00%	0.00%	NA
Indica I	595	96.10%	3.90%	0.00%	0.00%	NA
Indica II	465	97.00%	2.40%	0.65%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.20%	0.25%	0.00%	NA
Temperate Japonica	767	3.30%	96.70%	0.00%	0.00%	NA
Tropical Japonica	504	23.80%	76.20%	0.00%	0.00%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	54.40%	43.30%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0612517051	G -> A	LOC_Os06g21680.1	upstream_gene_variant ; 2366.0bp to feature; MODIFIER	silent_mutation	Average:19.394; most accessible tissue: Minghui63 flag leaf, score: 35.832	N	N	N	N
vg0612517051	G -> A	LOC_Os06g21670.1	downstream_gene_variant ; 3714.0bp to feature; MODIFIER	silent_mutation	Average:19.394; most accessible tissue: Minghui63 flag leaf, score: 35.832	N	N	N	N
vg0612517051	G -> A	LOC_Os06g21680-LOC_Os06g21690	intergenic_region ; MODIFIER	silent_mutation	Average:19.394; most accessible tissue: Minghui63 flag leaf, score: 35.832	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0612517051	NA	8.16E-06	mr1083	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
vg0612517051	6.82E-06	NA	mr1970	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
vg0612517051	2.99E-06	NA	mr1973	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