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Detailed information for vg0505080082:

Variant ID: vg0505080082 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5080082
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGGCATGGCAAACAAAGTGTGGCCAACAATTTGTTGGCCACGAGTGTGGTAATGTTTAGCTAGAAAATGAGTATATGACATGTAGGCCCATGAAACAA[G/A]
AAAGTGTGGCTTGCCACAACTGAAACAAGCAACCAAACGCTAAGCTAACAATCTGTGGCATGCCTAACATGTGGTGTGGCAATGTGTGGCACCAAACCAA

Reverse complement sequence

TTGGTTTGGTGCCACACATTGCCACACCACATGTTAGGCATGCCACAGATTGTTAGCTTAGCGTTTGGTTGCTTGTTTCAGTTGTGGCAAGCCACACTTT[C/T]
TTGTTTCATGGGCCTACATGTCATATACTCATTTTCTAGCTAAACATTACCACACTCGTGGCCAACAAATTGTTGGCCACACTTTGTTTGCCATGCCACA

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	88.00%	6.50%	0.38%	5.14%	NA
All Indica	2759	98.60%	0.50%	0.07%	0.83%	NA
All Japonica	1512	86.20%	13.50%	0.13%	0.13%	NA
Aus	269	17.80%	0.00%	4.83%	77.32%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.90%	0.00%	0.22%	0.86%	NA
Indica III	913	99.00%	0.70%	0.00%	0.33%	NA
Indica Intermediate	786	97.10%	0.80%	0.13%	2.04%	NA
Temperate Japonica	767	82.50%	17.30%	0.13%	0.00%	NA
Tropical Japonica	504	88.50%	11.50%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	5.40%	0.41%	0.83%	NA
VI/Aromatic	96	6.20%	86.50%	1.04%	6.25%	NA
Intermediate	90	87.80%	7.80%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505080082	G -> DEL	N	N	silent_mutation	Average:71.279; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0505080082	G -> A	LOC_Os05g09120.1	downstream_gene_variant ; 3197.0bp to feature; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0505080082	G -> A	LOC_Os05g09120-LOC_Os05g09130	intergenic_region ; MODIFIER	silent_mutation	Average:71.279; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505080082	NA	3.59E-06	mr1057	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
vg0505080082	NA	2.05E-07	mr1382	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
vg0505080082	3.87E-06	3.86E-06	mr1885	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
vg0505080082	NA	2.83E-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
vg0505080082	NA	3.60E-10	mr1057_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
vg0505080082	NA	9.08E-16	mr1842_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