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Detailed information for vg0133452014:

Variant ID: vg0133452014 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 33452014
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTGATCCTAATGAATCTAGGTTTTCACCCGGAGAAATCTCTTGAAGTTGAGTTGAATGAGGGCTCCAGTAGCAACACCTTCGAGAAGGTGAACGGCGCC[C/A]
AAAGGGGTTACCGTTGCTAGCACCGAGAGCGGAGCAAGGCTTTTGCCTTGGAGCACCCATCAACCATAGCATCCAAGGCGGGAGCCACCAAATGTTACCT

Reverse complement sequence

AGGTAACATTTGGTGGCTCCCGCCTTGGATGCTATGGTTGATGGGTGCTCCAAGGCAAAAGCCTTGCTCCGCTCTCGGTGCTAGCAACGGTAACCCCTTT[G/T]
GGCGCCGTTCACCTTCTCGAAGGTGTTGCTACTGGAGCCCTCATTCAACTCAACTTCAAGAGATTTCTCCGGGTGAAAACCTAGATTCATTAGGATCAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	4.20%	0.00%	0.00%	NA
All Indica	2759	99.10%	0.90%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	35.70%	64.30%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.20%	2.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0133452014	C -> A	LOC_Os01g57854.1	upstream_gene_variant ; 1419.0bp to feature; MODIFIER	silent_mutation	Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904	N	N	N	N
vg0133452014	C -> A	LOC_Os01g57840.1	downstream_gene_variant ; 2666.0bp to feature; MODIFIER	silent_mutation	Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904	N	N	N	N
vg0133452014	C -> A	LOC_Os01g57840-LOC_Os01g57854	intergenic_region ; MODIFIER	silent_mutation	Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0133452014	NA	1.18E-06	mr1320	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
vg0133452014	4.95E-06	NA	mr1379_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
vg0133452014	NA	4.87E-08	mr1510_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