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Detailed information for vg0715057249:

Variant ID: vg0715057249 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15057249
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, A: 0.37, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCCCTTAATCGCTAGCATCCTCAGCCACGCATTCACAAGATAGTCAACTGTGTGAAGATCTCCTGGTGTTTGATCGATCACTTGTGGTTAACGCAAC[A/T]
TTATTGTTTTACTTTTTGTATATATAGGTACGGATATGGCGCATCATCGGATTGCAATATTATTTCAGTTTTCATATTGAATTCGATTTGTTTTTCAGTT

Reverse complement sequence

AACTGAAAAACAAATCGAATTCAATATGAAAACTGAAATAATATTGCAATCCGATGATGCGCCATATCCGTACCTATATATACAAAAAGTAAAACAATAA[T/A]
GTTGCGTTAACCACAAGTGATCGATCAAACACCAGGAGATCTTCACACAGTTGACTATCTTGTGAATGCGTGGCTGAGGATGCTAGCGATTAAGGGATAT

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	49.70%	40.20%	0.78%	9.29%	NA
All Indica	2759	29.50%	57.40%	1.30%	11.82%	NA
All Japonica	1512	93.50%	5.80%	0.00%	0.73%	NA
Aus	269	7.80%	69.90%	0.00%	22.30%	NA
Indica I	595	49.10%	44.00%	3.36%	3.53%	NA
Indica II	465	14.20%	78.30%	0.43%	7.10%	NA
Indica III	913	22.30%	66.40%	0.22%	11.06%	NA
Indica Intermediate	786	31.90%	44.80%	1.53%	21.76%	NA
Temperate Japonica	767	88.10%	11.00%	0.00%	0.91%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	50.00%	12.50%	0.00%	37.50%	NA
Intermediate	90	61.10%	31.10%	1.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715057249	A -> DEL	N	N	silent_mutation	Average:64.591; most accessible tissue: Callus, score: 76.953	N	N	N	N
vg0715057249	A -> T	LOC_Os07g26180.1	downstream_gene_variant ; 167.0bp to feature; MODIFIER	silent_mutation	Average:64.591; most accessible tissue: Callus, score: 76.953	N	N	N	N
vg0715057249	A -> T	LOC_Os07g26190.1	downstream_gene_variant ; 2625.0bp to feature; MODIFIER	silent_mutation	Average:64.591; most accessible tissue: Callus, score: 76.953	N	N	N	N
vg0715057249	A -> T	LOC_Os07g26180-LOC_Os07g26190	intergenic_region ; MODIFIER	silent_mutation	Average:64.591; most accessible tissue: Callus, score: 76.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715057249	5.82E-06	NA	mr1558	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