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Detailed information for vg0728019959:

Variant ID: vg0728019959 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28019959
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGGTGTATTTTACTCTAAATATTATTCATATGAAGGTGATCTTTTAACAGGTTTAGACATTACAGATGTAGCGTTGGTTTCCACCCTTTTAAACATGC[G/A]
TTAGATTCTTAGAGCAGGCCGCACAATAGCAGACTATTAGCCAGCTATAAATATATTTTAATGAGAAAAAGATAAGAGAGAAGAGCAGCGGGCTACAGAT

Reverse complement sequence

ATCTGTAGCCCGCTGCTCTTCTCTCTTATCTTTTTCTCATTAAAATATATTTATAGCTGGCTAATAGTCTGCTATTGTGCGGCCTGCTCTAAGAATCTAA[C/T]
GCATGTTTAAAAGGGTGGAAACCAACGCTACATCTGTAATGTCTAAACCTGTTAAAAGATCACCTTCATATGAATAATATTTAGAGTAAAATACACCGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.60%	19.80%	1.31%	2.24%	NA
All Indica	2759	68.10%	26.40%	1.74%	3.84%	NA
All Japonica	1512	97.30%	2.50%	0.20%	0.00%	NA
Aus	269	46.50%	52.00%	1.49%	0.00%	NA
Indica I	595	77.80%	19.80%	2.35%	0.00%	NA
Indica II	465	76.80%	22.60%	0.43%	0.22%	NA
Indica III	913	55.40%	32.20%	1.97%	10.41%	NA
Indica Intermediate	786	70.20%	26.70%	1.78%	1.27%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	93.30%	6.30%	0.40%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	78.10%	19.80%	2.08%	0.00%	NA
Intermediate	90	78.90%	15.60%	5.56%	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
vg0728019959	G -> DEL	N	N	silent_mutation	Average:50.262; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0728019959	G -> A	LOC_Os07g46870.1	upstream_gene_variant ; 631.0bp to feature; MODIFIER	silent_mutation	Average:50.262; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0728019959	G -> A	LOC_Os07g46860-LOC_Os07g46870	intergenic_region ; MODIFIER	silent_mutation	Average:50.262; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728019959	NA	5.29E-06	mr1389_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
vg0728019959	NA	1.80E-06	mr1389_2	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
vg0728019959	2.68E-06	NA	mr1457_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
vg0728019959	8.60E-07	2.28E-09	mr1457_2	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