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Detailed information for vg0523767761:

Variant ID: vg0523767761 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23767761
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGATGAGAGGTTAAGGCGCTATTCTCGCAAGATTTTTTGCCCCACATGCCGACCATGTATGTATTTCGTCTATTATTCTTGCCGTTAGTTGAGGGAT[T/A]
TGAAGTTCTTTATCTTTGAAAACTCGCATGTTCCTCTCGCACCAGATTTCCCAACTCAAGAGCATGTGCAGTGACTGCATCCCCTTACTTTGACATTTGC

Reverse complement sequence

GCAAATGTCAAAGTAAGGGGATGCAGTCACTGCACATGCTCTTGAGTTGGGAAATCTGGTGCGAGAGGAACATGCGAGTTTTCAAAGATAAAGAACTTCA[A/T]
ATCCCTCAACTAACGGCAAGAATAATAGACGAAATACATACATGGTCGGCATGTGGGGCAAAAAATCTTGCGAGAATAGCGCCTTAACCTCTCATCCTTT

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	98.20%	1.50%	0.36%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	95.00%	4.00%	0.93%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	0.00%	1.04%	0.00%	NA
Tropical Japonica	504	87.90%	11.10%	0.99%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0523767761	T -> A	LOC_Os05g40450.1	downstream_gene_variant ; 4758.0bp to feature; MODIFIER	silent_mutation	Average:41.135; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0523767761	T -> A	LOC_Os05g40470.1	downstream_gene_variant ; 1481.0bp to feature; MODIFIER	silent_mutation	Average:41.135; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0523767761	T -> A	LOC_Os05g40480.1	downstream_gene_variant ; 3892.0bp to feature; MODIFIER	silent_mutation	Average:41.135; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0523767761	T -> A	LOC_Os05g40460.1	intron_variant ; MODIFIER	silent_mutation	Average:41.135; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523767761	1.18E-06	2.68E-08	mr1125	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
vg0523767761	NA	5.07E-08	mr1136	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
vg0523767761	NA	1.25E-07	mr1188	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
vg0523767761	1.85E-07	9.71E-10	mr1448	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
vg0523767761	1.92E-06	2.15E-10	mr1125_2	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
vg0523767761	3.16E-06	7.98E-10	mr1188_2	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
vg0523767761	9.98E-06	9.97E-06	mr1448_2	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