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Detailed information for vg0127858725:

Variant ID: vg0127858725 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27858725
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: 359. )

Flanking Sequence (100 bp) in Reference Genome:

AAACCTAAGACATGCATGTGGTTTGTTGAGAAGTTGGGTTGTAACTATGGGTTGCAATTATTATGTTTGTCTTCCAATCATATATTCATGTTCGCATATC[T/A]
AAATCATGTATGCATGGGAGTTCTAATTATAGCTTGGAGCTAGTTTTTTCCCCTTATAACCGTACTATTAGCTTTTGTGGTGATCAACATTTTTTTTGGG

Reverse complement sequence

CCCAAAAAAAATGTTGATCACCACAAAAGCTAATAGTACGGTTATAAGGGGAAAAAACTAGCTCCAAGCTATAATTAGAACTCCCATGCATACATGATTT[A/T]
GATATGCGAACATGAATATATGATTGGAAGACAAACATAATAATTGCAACCCATAGTTACAACCCAACTTCTCAACAAACCACATGCATGTCTTAGGTTT

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	97.50%	2.30%	0.23%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.30%	7.00%	0.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	78.00%	20.80%	1.19%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0127858725	T -> A	LOC_Os01g48570.1	downstream_gene_variant ; 2728.0bp to feature; MODIFIER	silent_mutation	Average:46.02; most accessible tissue: Zhenshan97 flower, score: 73.414	N	N	N	N
vg0127858725	T -> A	LOC_Os01g48580.1	intron_variant ; MODIFIER	silent_mutation	Average:46.02; most accessible tissue: Zhenshan97 flower, score: 73.414	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127858725	NA	1.29E-07	mr1042_2	Jap_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
vg0127858725	1.18E-07	4.54E-10	mr1871_2	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