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Detailed information for vg0528849908:

Variant ID: vg0528849908 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28849908
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATTTACTCCCTCTGTTTCACAATGTAAGTCATTCTATCATTTTCCACATTTATATTGATATATATATATATATATTCATTAACATCAATATGAATGT[G/A]
GAAAATGCTAGAACGACTTATATTGTGAAACGGAGGAAGTATTTCAGAATAGATTAAGTATTAAATTTATGGTTGGCATTACGAGTGCGCGGTACTGATG

Reverse complement sequence

CATCAGTACCGCGCACTCGTAATGCCAACCATAAATTTAATACTTAATCTATTCTGAAATACTTCCTCCGTTTCACAATATAAGTCGTTCTAGCATTTTC[C/T]
ACATTCATATTGATGTTAATGAATATATATATATATATATCAATATAAATGTGGAAAATGATAGAATGACTTACATTGTGAAACAGAGGGAGTAAATAAT

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	84.80%	14.10%	0.25%	0.83%	NA
All Indica	2759	74.90%	23.30%	0.43%	1.38%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	32.60%	63.20%	1.01%	3.19%	NA
Indica II	465	75.50%	22.80%	0.43%	1.29%	NA
Indica III	913	98.80%	1.20%	0.00%	0.00%	NA
Indica Intermediate	786	78.90%	19.00%	0.51%	1.65%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	16.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0528849908	G -> DEL	N	N	silent_mutation	Average:46.211; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0528849908	G -> A	LOC_Os05g50340.1	upstream_gene_variant ; 3858.0bp to feature; MODIFIER	silent_mutation	Average:46.211; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0528849908	G -> A	LOC_Os05g50360.1	upstream_gene_variant ; 4897.0bp to feature; MODIFIER	silent_mutation	Average:46.211; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0528849908	G -> A	LOC_Os05g50350.1	intron_variant ; MODIFIER	silent_mutation	Average:46.211; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528849908	2.59E-06	2.59E-06	mr1273_2	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
vg0528849908	8.52E-06	8.52E-06	mr1273_2	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