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Detailed information for vg0515200651:

Variant ID: vg0515200651 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15200651
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: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCAGCCAGTAAACTAGCAGAGACAACACTCCTCATTTTTTAAGGCCTCTAGTATTGTTGTGTTTATTTTTGTACACTTCTATGAATCTTTCTATGAC[T/A]
TGCAGTCAAGAAGATATGTAAAGTCTTCTTTTTCGAACGGTCAGACCGTTGCCGACGTTTTATATTAAGAAGAAGATATCCCATTTTGAGGAGAAAACGG

Reverse complement sequence

CCGTTTTCTCCTCAAAATGGGATATCTTCTTCTTAATATAAAACGTCGGCAACGGTCTGACCGTTCGAAAAAGAAGACTTTACATATCTTCTTGACTGCA[A/T]
GTCATAGAAAGATTCATAGAAGTGTACAAAAATAAACACAACAATACTAGAGGCCTTAAAAAATGAGGAGTGTTGTCTCTGCTAGTTTACTGGCTGAAGA

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	72.30%	4.70%	3.55%	19.36%	NA
All Indica	2759	60.50%	3.60%	5.36%	30.59%	NA
All Japonica	1512	97.90%	0.10%	0.73%	1.32%	NA
Aus	269	37.20%	45.00%	2.23%	15.61%	NA
Indica I	595	65.20%	1.70%	6.22%	26.89%	NA
Indica II	465	66.00%	1.90%	3.23%	28.82%	NA
Indica III	913	64.40%	6.10%	5.37%	24.10%	NA
Indica Intermediate	786	49.00%	3.10%	5.98%	41.98%	NA
Temperate Japonica	767	97.90%	0.00%	1.17%	0.91%	NA
Tropical Japonica	504	97.80%	0.20%	0.00%	1.98%	NA
Japonica Intermediate	241	97.90%	0.00%	0.83%	1.24%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	2.20%	3.33%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515200651	T -> DEL	N	N	silent_mutation	Average:32.627; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0515200651	T -> A	LOC_Os05g26130.1	upstream_gene_variant ; 3260.0bp to feature; MODIFIER	silent_mutation	Average:32.627; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0515200651	T -> A	LOC_Os05g26130-LOC_Os05g26140	intergenic_region ; MODIFIER	silent_mutation	Average:32.627; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515200651	5.85E-07	1.32E-07	mr1413	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
vg0515200651	9.36E-07	9.36E-07	mr1413	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
vg0515200651	NA	1.76E-06	mr1574	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