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Detailed information for vg0336013947:

Variant ID: vg0336013947 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 36013947
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGCGCCGTCACTCGTAGACTACTCCATCCCGCTCGCCGTCGTGCACCTGCGATCGGGAGAGCAGGTCTCTGGAACCTCTGCCTTCGACGTCTTGCACC[G/A]
GGAGAAGGCGGCAATAAGGTTTTTGGGAAGCACTTCGCGCGACTGCTCCCTGTTCGTCCGCGACGGCTCGCCTTCCTCTCCGCTTGCGTGCTACGCGCCT

Reverse complement sequence

AGGCGCGTAGCACGCAAGCGGAGAGGAAGGCGAGCCGTCGCGGACGAACAGGGAGCAGTCGCGCGAAGTGCTTCCCAAAAACCTTATTGCCGCCTTCTCC[C/T]
GGTGCAAGACGTCGAAGGCAGAGGTTCCAGAGACCTGCTCTCCCGATCGCAGGTGCACGACGGCGAGCGGGATGGAGTAGTCTACGAGTGACGGCGCAGC

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	97.80%	1.00%	1.12%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.14%	0.00%	NA
All Japonica	1512	94.00%	2.70%	3.24%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.30%	0.50%	0.11%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	91.70%	3.10%	5.22%	0.00%	NA
Tropical Japonica	504	96.60%	2.40%	0.99%	0.00%	NA
Japonica Intermediate	241	96.30%	2.10%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0336013947	G -> A	LOC_Os03g63780.1	upstream_gene_variant ; 354.0bp to feature; MODIFIER	silent_mutation	Average:44.041; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N
vg0336013947	G -> A	LOC_Os03g63790.1	upstream_gene_variant ; 4808.0bp to feature; MODIFIER	silent_mutation	Average:44.041; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N
vg0336013947	G -> A	LOC_Os03g63770-LOC_Os03g63780	intergenic_region ; MODIFIER	silent_mutation	Average:44.041; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0336013947	7.79E-06	7.79E-06	mr1924	Jap_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
vg0336013947	2.22E-07	2.22E-07	mr1004_2	Jap_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