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Detailed information for vg0524150578:

Variant ID: vg0524150578 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 24150578
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.03, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CGAAGCGATTTCCCTAACCCAAGATAGCAAAAGACAGAAAGAGTCAATAAAAACTCCATGTAACTGATGGGCTTGGCATTAAAAAAAAAAAAACTGATGG[T/G]
CTTGCAACTCTCTACAAAGAGAAGCACTAGCAAATTAAACTACATTGACATTAGTCTGCTAAATGTGCCTTTTCATTTCTTTCTTGACAACAATAACAAA

Reverse complement sequence

TTTGTTATTGTTGTCAAGAAAGAAATGAAAAGGCACATTTAGCAGACTAATGTCAATGTAGTTTAATTTGCTAGTGCTTCTCTTTGTAGAGAGTTGCAAG[A/C]
CCATCAGTTTTTTTTTTTTTAATGCCAAGCCCATCAGTTACATGGAGTTTTTATTGACTCTTTCTGTCTTTTGCTATCTTGGGTTAGGGAAATCGCTTCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.00%	49.20%	0.53%	0.21%	NA
All Indica	2759	27.40%	71.40%	0.83%	0.36%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	0.40%	99.60%	0.00%	0.00%	NA
Indica I	595	19.20%	78.20%	2.18%	0.50%	NA
Indica II	465	31.80%	67.70%	0.43%	0.00%	NA
Indica III	913	31.30%	67.80%	0.33%	0.55%	NA
Indica Intermediate	786	26.60%	72.50%	0.64%	0.25%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	63.50%	36.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	48.90%	2.22%	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
vg0524150578	T -> DEL	N	N	silent_mutation	Average:71.253; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0524150578	T -> G	LOC_Os05g41240.1	downstream_gene_variant ; 3155.0bp to feature; MODIFIER	silent_mutation	Average:71.253; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0524150578	T -> G	LOC_Os05g41240.3	downstream_gene_variant ; 3155.0bp to feature; MODIFIER	silent_mutation	Average:71.253; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0524150578	T -> G	LOC_Os05g41240.2	downstream_gene_variant ; 3155.0bp to feature; MODIFIER	silent_mutation	Average:71.253; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0524150578	T -> G	LOC_Os05g41230.1	intron_variant ; MODIFIER	silent_mutation	Average:71.253; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524150578	NA	3.57E-06	mr1004	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