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Detailed information for vg0115383222:

Variant ID: vg0115383222 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15383222
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.09, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCCCACTGATGGAAAGTATATCGGATATGGTTTGTGTGGCATATATTACTGCTGAAAACTCCCTCCCAAGTAGGCCTACAACAATAAAAGAAAGAAGA[T/A]
TAGTCTATGCTTGCCGATGACAATGGTTTGAAGGTTGACAAATTAAGCAATGAATTTTACAATCCCATAGGAAAGTATACTACAGTTATCCTGCATTCAG

Reverse complement sequence

CTGAATGCAGGATAACTGTAGTATACTTTCCTATGGGATTGTAAAATTCATTGCTTAATTTGTCAACCTTCAAACCATTGTCATCGGCAAGCATAGACTA[A/T]
TCTTCTTTCTTTTATTGTTGTAGGCCTACTTGGGAGGGAGTTTTCAGCAGTAATATATGCCACACAAACCATATCCGATATACTTTCCATCAGTGGGGGA

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	47.80%	9.40%	37.13%	5.63%	NA
All Indica	2759	21.60%	13.80%	55.49%	9.13%	NA
All Japonica	1512	97.40%	0.30%	2.12%	0.13%	NA
Aus	269	35.70%	17.50%	44.24%	2.60%	NA
Indica I	595	8.60%	12.10%	57.48%	21.85%	NA
Indica II	465	17.60%	13.30%	57.20%	11.83%	NA
Indica III	913	30.00%	16.30%	52.90%	0.77%	NA
Indica Intermediate	786	23.90%	12.50%	55.98%	7.63%	NA
Temperate Japonica	767	99.10%	0.30%	0.65%	0.00%	NA
Tropical Japonica	504	94.80%	0.60%	4.37%	0.20%	NA
Japonica Intermediate	241	97.50%	0.00%	2.07%	0.41%	NA
VI/Aromatic	96	42.70%	8.30%	48.96%	0.00%	NA
Intermediate	90	60.00%	5.60%	28.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115383222	T -> A	LOC_Os01g27560.1	downstream_gene_variant ; 1212.0bp to feature; MODIFIER	silent_mutation	Average:22.544; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0115383222	T -> A	LOC_Os01g27570.1	downstream_gene_variant ; 1675.0bp to feature; MODIFIER	silent_mutation	Average:22.544; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0115383222	T -> A	LOC_Os01g27580.1	downstream_gene_variant ; 4231.0bp to feature; MODIFIER	silent_mutation	Average:22.544; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0115383222	T -> A	LOC_Os01g27560-LOC_Os01g27570	intergenic_region ; MODIFIER	silent_mutation	Average:22.544; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0115383222	T -> DEL	N	N	silent_mutation	Average:22.544; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115383222	NA	6.28E-10	mr1705_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
vg0115383222	NA	4.14E-07	mr1819_2	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