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Detailed information for vg0520634158:

Variant ID: vg0520634158 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20634158
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCCTCCATCCCATAATAGGTGACGTTTTTGACTTTTTATTTGCAACGTTTGACCATTCGTTTTATTTGAAAAATTAGTGCAAATATAAAAAAAGATAA[G/A]
TCATATGTAAAGTACTTTTGATAATAAAGCAAATGACAAACAAAATAAATAATAATTCTAAATTTTTTTGAATAAGACGAATGATCAAACATTGACAAAC

Reverse complement sequence

GTTTGTCAATGTTTGATCATTCGTCTTATTCAAAAAAATTTAGAATTATTATTTATTTTGTTTGTCATTTGCTTTATTATCAAAAGTACTTTACATATGA[C/T]
TTATCTTTTTTTATATTTGCACTAATTTTTCAAATAAAACGAATGGTCAAACGTTGCAAATAAAAAGTCAAAAACGTCACCTATTATGGGATGGAGGGAG

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	93.10%	6.80%	0.13%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	82.90%	16.80%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	70.70%	28.70%	0.65%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	14.10%	0.00%	0.00%	NA
VI/Aromatic	96	39.60%	59.40%	1.04%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0520634158	G -> A	LOC_Os05g34780.1	upstream_gene_variant ; 2224.0bp to feature; MODIFIER	silent_mutation	Average:62.163; most accessible tissue: Minghui63 flower, score: 76.594	N	N	N	N
vg0520634158	G -> A	LOC_Os05g34770.1	downstream_gene_variant ; 1708.0bp to feature; MODIFIER	silent_mutation	Average:62.163; most accessible tissue: Minghui63 flower, score: 76.594	N	N	N	N
vg0520634158	G -> A	LOC_Os05g34770-LOC_Os05g34780	intergenic_region ; MODIFIER	silent_mutation	Average:62.163; most accessible tissue: Minghui63 flower, score: 76.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520634158	3.92E-06	NA	mr1404	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
vg0520634158	NA	6.92E-06	mr1913	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