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Detailed information for vg0516598900:

Variant ID: vg0516598900 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16598900
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGATTCAGAACATCCAACCCCTAGCTAACCAGTCACGCACTTAAGAAACTTTCATTCCCGAGATTAAATTAATGTCCATTAAGTACACAAGTCAACACC[A/G]
CTCACCATCTACAAAAATCAGTACTCCCTCCATTCCAAAATACACTTATCCCAAAAACCAAAAGATAATTATTTCGCCTACTCGTCTGAATTATTTTATA

Reverse complement sequence

TATAAAATAATTCAGACGAGTAGGCGAAATAATTATCTTTTGGTTTTTGGGATAAGTGTATTTTGGAATGGAGGGAGTACTGATTTTTGTAGATGGTGAG[T/C]
GGTGTTGACTTGTGTACTTAATGGACATTAATTTAATCTCGGGAATGAAAGTTTCTTAAGTGCGTGACTGGTTAGCTAGGGGTTGGATGTTCTGAATCTT

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	95.90%	3.70%	0.38%	0.00%	NA
All Indica	2759	99.60%	0.20%	0.18%	0.00%	NA
All Japonica	1512	88.70%	10.40%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.70%	0.50%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	79.00%	19.40%	1.56%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	3.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	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
vg0516598900	A -> G	LOC_Os05g28350.1	downstream_gene_variant ; 1697.0bp to feature; MODIFIER	silent_mutation	Average:38.297; most accessible tissue: Callus, score: 80.566	N	N	N	N
vg0516598900	A -> G	LOC_Os05g28340-LOC_Os05g28350	intergenic_region ; MODIFIER	silent_mutation	Average:38.297; most accessible tissue: Callus, score: 80.566	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516598900	6.10E-07	6.10E-07	mr1955	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