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Detailed information for vg0315761422:

Variant ID: vg0315761422 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15761422
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CTTAGTCGTACGCTATGTACTTTCTTGGTTGACGTCGGAGATTGACTCAGACAAACCCTTTAGGTGCCCGCACGAGGCTGACAAAGGAAGTCTAACGTTA[T/A]
CTCTGAACTCACCGAGAACGGTCACATGAGCTCGATAACAGTTACTCCAAGGTCTGCGCGCGCTTGAGAATATGAATTCGTTCATTTGCATTGAAGTCGG

Reverse complement sequence

CCGACTTCAATGCAAATGAACGAATTCATATTCTCAAGCGCGCGCAGACCTTGGAGTAACTGTTATCGAGCTCATGTGACCGTTCTCGGTGAGTTCAGAG[A/T]
TAACGTTAGACTTCCTTTGTCAGCCTCGTGCGGGCACCTAAAGGGTTTGTCTGAGTCAATCTCCGACGTCAACCAAGAAAGTACATAGCGTACGACTAAG

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	43.70%	0.30%	3.22%	52.79%	NA
All Indica	2759	23.10%	0.10%	2.54%	74.30%	NA
All Japonica	1512	76.20%	0.90%	3.17%	19.78%	NA
Aus	269	58.00%	0.40%	11.15%	30.48%	NA
Indica I	595	26.40%	0.00%	3.19%	70.42%	NA
Indica II	465	11.80%	0.00%	2.58%	85.59%	NA
Indica III	913	23.80%	0.00%	2.52%	73.71%	NA
Indica Intermediate	786	26.50%	0.30%	2.04%	71.25%	NA
Temperate Japonica	767	96.00%	0.00%	0.26%	3.78%	NA
Tropical Japonica	504	46.20%	2.60%	8.53%	42.66%	NA
Japonica Intermediate	241	75.90%	0.00%	1.24%	22.82%	NA
VI/Aromatic	96	81.20%	0.00%	2.08%	16.67%	NA
Intermediate	90	44.40%	0.00%	2.22%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315761422	T -> A	LOC_Os03g27470.1	downstream_gene_variant ; 2546.0bp to feature; MODIFIER	silent_mutation	Average:27.835; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0315761422	T -> A	LOC_Os03g27480.1	downstream_gene_variant ; 1980.0bp to feature; MODIFIER	silent_mutation	Average:27.835; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0315761422	T -> A	LOC_Os03g27480.2	downstream_gene_variant ; 2140.0bp to feature; MODIFIER	silent_mutation	Average:27.835; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0315761422	T -> A	LOC_Os03g27470-LOC_Os03g27480	intergenic_region ; MODIFIER	silent_mutation	Average:27.835; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N
vg0315761422	T -> DEL	N	N	silent_mutation	Average:27.835; most accessible tissue: Minghui63 young leaf, score: 43.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315761422	2.85E-06	2.85E-06	mr1848	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