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Detailed information for vg0517768858:

Variant ID: vg0517768858 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17768858
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTTCTTTTTTTTCACTCTCATGGGATAAAAACCAAATTAATAAATTCAGCCAACAGTTGTAAAAATATATGTTATTCCGAGTTGTATTCTAGCACAA[G/A]
TCCATTAAACTTCCTATGAATGCACAAGTCGCCATGTGACATCCTACATACTCTCCTAAGCCGTCACGTGACACTCTAAGAAATTAGAAAAAATCTTAAA

Reverse complement sequence

TTTAAGATTTTTTCTAATTTCTTAGAGTGTCACGTGACGGCTTAGGAGAGTATGTAGGATGTCACATGGCGACTTGTGCATTCATAGGAAGTTTAATGGA[C/T]
TTGTGCTAGAATACAACTCGGAATAACATATATTTTTACAACTGTTGGCTGAATTTATTAATTTGGTTTTTATCCCATGAGAGTGAAAAAAAAGAAAAAA

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	89.30%	3.30%	1.78%	5.63%	NA
All Indica	2759	92.20%	0.10%	0.98%	6.78%	NA
All Japonica	1512	81.70%	10.10%	3.51%	4.70%	NA
Aus	269	98.10%	0.00%	0.00%	1.86%	NA
Indica I	595	91.10%	0.00%	1.34%	7.56%	NA
Indica II	465	92.70%	0.00%	1.94%	5.38%	NA
Indica III	913	91.20%	0.10%	0.33%	8.32%	NA
Indica Intermediate	786	93.80%	0.10%	0.89%	5.22%	NA
Temperate Japonica	767	82.70%	11.60%	3.78%	1.96%	NA
Tropical Japonica	504	84.30%	3.00%	1.59%	11.11%	NA
Japonica Intermediate	241	73.40%	19.90%	6.64%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	92.20%	3.30%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517768858	G -> DEL	N	N	silent_mutation	Average:12.925; most accessible tissue: Callus, score: 34.613	N	N	N	N
vg0517768858	G -> A	LOC_Os05g30680.1	downstream_gene_variant ; 1322.0bp to feature; MODIFIER	silent_mutation	Average:12.925; most accessible tissue: Callus, score: 34.613	N	N	N	N
vg0517768858	G -> A	LOC_Os05g30680-LOC_Os05g30690	intergenic_region ; MODIFIER	silent_mutation	Average:12.925; most accessible tissue: Callus, score: 34.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517768858	9.01E-07	9.01E-07	mr1181_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