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Detailed information for vg0205657255:

Variant ID: vg0205657255 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5657255
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCTGTTTTATGTGATGAGCGTAGATAGGATGGTATAAGGTTTTTTTTCTTTTTGACATAACTCAAACTCTGGAAGTTGAACTTTTTTTAAGACGGAGA[G/A]
AGTAGATGGTTAATATAATACTAAATTAAATCACAATATCCATAAATACAATATTGTGTGTATCTTTGGTGAATGCAAAGGCTGAAAATTACTTCTTTTG

Reverse complement sequence

CAAAAGAAGTAATTTTCAGCCTTTGCATTCACCAAAGATACACACAATATTGTATTTATGGATATTGTGATTTAATTTAGTATTATATTAACCATCTACT[C/T]
TCTCCGTCTTAAAAAAAGTTCAACTTCCAGAGTTTGAGTTATGTCAAAAAGAAAAAAAACCTTATACCATCCTATCTACGCTCATCACATAAAACAGGAA

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	86.50%	13.50%	0.02%	0.00%	NA
All Indica	2759	89.50%	10.40%	0.04%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	88.40%	11.60%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	86.40%	13.60%	0.00%	0.00%	NA
Indica Intermediate	786	89.60%	10.30%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	39.60%	60.40%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0205657255	G -> A	LOC_Os02g10730.1	upstream_gene_variant ; 1761.0bp to feature; MODIFIER	silent_mutation	Average:41.675; most accessible tissue: Callus, score: 65.522	N	N	N	N
vg0205657255	G -> A	LOC_Os02g10730-LOC_Os02g10740	intergenic_region ; MODIFIER	silent_mutation	Average:41.675; most accessible tissue: Callus, score: 65.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205657255	NA	2.12E-06	mr1006	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
vg0205657255	NA	1.66E-06	mr1052	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
vg0205657255	NA	3.44E-06	mr1073	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
vg0205657255	NA	5.60E-13	mr1522	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
vg0205657255	NA	9.47E-16	mr1765	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
vg0205657255	NA	6.98E-13	mr1918	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
vg0205657255	NA	2.60E-08	mr1929	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
vg0205657255	2.62E-06	NA	mr1037_2	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
vg0205657255	2.86E-06	3.98E-08	mr1037_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
vg0205657255	NA	6.77E-06	mr1096_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
vg0205657255	NA	5.00E-07	mr1126_2	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
vg0205657255	NA	9.27E-09	mr1166_2	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
vg0205657255	NA	1.03E-06	mr1929_2	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