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Detailed information for vg0209233917:

Variant ID: vg0209233917 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9233917
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCCTTAACTTGGATAAACAGGAGAATAGCATATGCATAAAAATTCTGTGATGTTCTCTAAACAGGAGAAACATTGCAAGTAGTTACAATGATGTCTATC[T/A]
GAATCTTAGCCTAGAGCTAGTTGCCTTCATTTGCCTCGGTCACTAGGCGTTTAATATCTTGCTGCACTTCAATCACTTCGTTCATAGTAGAATTAATGAG

Reverse complement sequence

CTCATTAATTCTACTATGAACGAAGTGATTGAAGTGCAGCAAGATATTAAACGCCTAGTGACCGAGGCAAATGAAGGCAACTAGCTCTAGGCTAAGATTC[A/T]
GATAGACATCATTGTAACTACTTGCAATGTTTCTCCTGTTTAGAGAACATCACAGAATTTTTATGCATATGCTATTCTCCTGTTTATCCAAGTTAAGGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	0.20%	2.16%	18.87%	NA
All Indica	2759	65.40%	0.30%	3.59%	30.74%	NA
All Japonica	1512	98.10%	0.00%	0.07%	1.79%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	64.90%	0.00%	1.85%	33.28%	NA
Indica II	465	63.40%	0.40%	3.44%	32.69%	NA
Indica III	913	69.30%	0.30%	4.93%	25.41%	NA
Indica Intermediate	786	62.50%	0.30%	3.44%	33.84%	NA
Temperate Japonica	767	98.20%	0.00%	0.00%	1.83%	NA
Tropical Japonica	504	98.00%	0.00%	0.20%	1.79%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	0.00%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209233917	T -> A	LOC_Os02g16250.1	upstream_gene_variant ; 4522.0bp to feature; MODIFIER	silent_mutation	Average:7.041; most accessible tissue: Callus, score: 29.807	N	N	N	N
vg0209233917	T -> A	LOC_Os02g16240.1	downstream_gene_variant ; 17.0bp to feature; MODIFIER	silent_mutation	Average:7.041; most accessible tissue: Callus, score: 29.807	N	N	N	N
vg0209233917	T -> A	LOC_Os02g16230-LOC_Os02g16240	intergenic_region ; MODIFIER	silent_mutation	Average:7.041; most accessible tissue: Callus, score: 29.807	N	N	N	N
vg0209233917	T -> DEL	N	N	silent_mutation	Average:7.041; most accessible tissue: Callus, score: 29.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209233917	2.08E-06	3.28E-06	mr1685	Ind_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
vg0209233917	NA	1.09E-06	mr1706	Ind_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