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Detailed information for vg0524150176:

Variant ID: vg0524150176 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 24150176
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AGGTTTGACAGCCCAGCCAGCTCGTTTGGGATTGGCCCAGTTAAAAGGTTGTGATCAATTCTCCTGCCAAGAGTAAAGAAAAAACAAAAACTCAAACATA[G/A]
ATATCAAAGTACATTTTGCATAGCTGAACAGTACTTTCTGATTTCAGATATAAGTTTTTTTTAAGACTTGTGCACATGAACTTACATTAATTACAGATAA

Reverse complement sequence

TTATCTGTAATTAATGTAAGTTCATGTGCACAAGTCTTAAAAAAAACTTATATCTGAAATCAGAAAGTACTGTTCAGCTATGCAAAATGTACTTTGATAT[C/T]
TATGTTTGAGTTTTTGTTTTTTCTTTACTCTTGGCAGGAGAATTGATCACAACCTTTTAACTGGGCCAATCCCAAACGAGCTGGCTGGGCTGTCAAACCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	49.80%	0.06%	0.25%	NA
All Indica	2759	72.30%	27.10%	0.11%	0.43%	NA
All Japonica	1512	0.70%	99.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	80.80%	19.20%	0.00%	0.00%	NA
Indica II	465	68.20%	30.80%	0.22%	0.86%	NA
Indica III	913	68.50%	31.00%	0.00%	0.55%	NA
Indica Intermediate	786	72.90%	26.50%	0.25%	0.38%	NA
Temperate Japonica	767	0.00%	100.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	98.00%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	36.50%	63.50%	0.00%	0.00%	NA
Intermediate	90	52.20%	47.80%	0.00%	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
vg0524150176	G -> DEL	N	N	silent_mutation	Average:71.287; most accessible tissue: Callus, score: 94.373	N	N	N	N
vg0524150176	G -> A	LOC_Os05g41240.1	downstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:71.287; most accessible tissue: Callus, score: 94.373	N	N	N	N
vg0524150176	G -> A	LOC_Os05g41240.3	downstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:71.287; most accessible tissue: Callus, score: 94.373	N	N	N	N
vg0524150176	G -> A	LOC_Os05g41240.2	downstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:71.287; most accessible tissue: Callus, score: 94.373	N	N	N	N
vg0524150176	G -> A	LOC_Os05g41230.1	intron_variant ; MODIFIER	silent_mutation	Average:71.287; most accessible tissue: Callus, score: 94.373	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524150176	NA	3.54E-06	mr1004	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