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Detailed information for vg0516131571:

Variant ID: vg0516131571 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16131571
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.05, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTCCTCCTTGAATCCAATCTTCCAAGGATCACCCCTTTCCCTCGTGTTCGTCCTAGATGATCGGGAGTCTGCAGGGCGAGTGATAGCTCGTCCTTCTC[A/T]
CTGTCAGGTCGGAACGTGCCCTGAGAAGAGGCTTCCACTGCATCCGTTAGTCGACTGGCAGCCTCTGATCGCTGAAGACTAGGGAGCCATCAACTGGGTT

Reverse complement sequence

AACCCAGTTGATGGCTCCCTAGTCTTCAGCGATCAGAGGCTGCCAGTCGACTAACGGATGCAGTGGAAGCCTCTTCTCAGGGCACGTTCCGACCTGACAG[T/A]
GAGAAGGACGAGCTATCACTCGCCCTGCAGACTCCCGATCATCTAGGACGAACACGAGGGAAAGGGGTGATCCTTGGAAGATTGGATTCAAGGAGGACAT

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	28.40%	17.20%	1.90%	52.52%	NA
All Indica	2759	29.60%	1.70%	1.96%	66.76%	NA
All Japonica	1512	26.20%	49.30%	0.13%	24.34%	NA
Aus	269	1.50%	0.40%	12.27%	85.87%	NA
Indica I	595	30.90%	3.40%	1.34%	64.37%	NA
Indica II	465	17.20%	2.60%	2.80%	77.42%	NA
Indica III	913	30.00%	0.10%	1.53%	68.35%	NA
Indica Intermediate	786	35.40%	1.80%	2.42%	60.43%	NA
Temperate Japonica	767	7.80%	85.30%	0.00%	6.91%	NA
Tropical Japonica	504	41.10%	5.60%	0.40%	52.98%	NA
Japonica Intermediate	241	53.50%	26.60%	0.00%	19.92%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	35.60%	21.10%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0516131571	A -> T	LOC_Os05g27680.1	upstream_gene_variant ; 3363.0bp to feature; MODIFIER	silent_mutation	Average:61.764; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N
vg0516131571	A -> T	LOC_Os05g27700.1	downstream_gene_variant ; 2913.0bp to feature; MODIFIER	silent_mutation	Average:61.764; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N
vg0516131571	A -> T	LOC_Os05g27690.1	intron_variant ; MODIFIER	silent_mutation	Average:61.764; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N
vg0516131571	A -> DEL	N	N	silent_mutation	Average:61.764; most accessible tissue: Minghui63 flag leaf, score: 80.786	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516131571	1.93E-06	7.78E-06	mr1528	Ind_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
vg0516131571	NA	8.83E-06	mr1113_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