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Detailed information for vg0117784588:

Variant ID: vg0117784588 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17784588
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCGTGAGGCGCCATGTCAGAATGATCCCAGGAAATCGATATCTGATATAGCGCCGGGGGCTACTGTCGAAGATATGGGCCCGGGGGTATGTGAAGTAG[A/T]
GGGGAATTACTTTCCCTCCGGCCACGTGACTCTACAGGCTGCCCTACTCAAGCGTCACGCGAGTCGTGGATGCGGCGCGGCGCGGGGGGGGGGGGGGGGG

Reverse complement sequence

CCCCCCCCCCCCCCCCCGCGCCGCGCCGCATCCACGACTCGCGTGACGCTTGAGTAGGGCAGCCTGTAGAGTCACGTGGCCGGAGGGAAAGTAATTCCCC[T/A]
CTACTTCACATACCCCCGGGCCCATATCTTCGACAGTAGCCCCCGGCGCTATATCAGATATCGATTTCCTGGGATCATTCTGACATGGCGCCTCACGACT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.50%	31.30%	1.80%	25.39%	NA
All Indica	2759	8.60%	49.80%	2.68%	39.00%	NA
All Japonica	1512	97.50%	2.10%	0.00%	0.40%	NA
Aus	269	40.50%	19.00%	3.35%	37.17%	NA
Indica I	595	4.50%	37.10%	3.53%	54.79%	NA
Indica II	465	17.00%	47.30%	1.94%	33.76%	NA
Indica III	913	4.30%	64.50%	2.30%	28.92%	NA
Indica Intermediate	786	11.60%	43.60%	2.93%	41.86%	NA
Temperate Japonica	767	99.10%	0.80%	0.00%	0.13%	NA
Tropical Japonica	504	94.60%	4.60%	0.00%	0.79%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	2.10%	1.04%	2.08%	NA
Intermediate	90	57.80%	23.30%	1.11%	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
vg0117784588	A -> T	LOC_Os01g32410.1	upstream_gene_variant ; 4423.0bp to feature; MODIFIER	silent_mutation	Average:51.334; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0117784588	A -> T	LOC_Os01g32420.1	upstream_gene_variant ; 809.0bp to feature; MODIFIER	silent_mutation	Average:51.334; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0117784588	A -> T	LOC_Os01g32420-LOC_Os01g32430	intergenic_region ; MODIFIER	silent_mutation	Average:51.334; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N
vg0117784588	A -> DEL	N	N	silent_mutation	Average:51.334; most accessible tissue: Zhenshan97 flag leaf, score: 77.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117784588	NA	3.26E-10	mr1518	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
vg0117784588	NA	4.19E-09	mr1676	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