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Detailed information for vg0432568737:

Variant ID: vg0432568737 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32568737
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGGCTAGAGATTGAAATTCTAAGCACGACTTAATAGATCAAACTCAACTGATACAGCATTAAGTATGAAAAGAAGAACAATATCTAGACAATCAAGCC[G/A]
CTGGATGTTTTATAGAGTGGTGGATATCTCATATAATCTAAGCCAACATCGTTATTTAACCTAATCGGCTGCCTTCTATTAGCAGATGTTAGCCGATTGT

Reverse complement sequence

ACAATCGGCTAACATCTGCTAATAGAAGGCAGCCGATTAGGTTAAATAACGATGTTGGCTTAGATTATATGAGATATCCACCACTCTATAAAACATCCAG[C/T]
GGCTTGATTGTCTAGATATTGTTCTTCTTTTCATACTTAATGCTGTATCAGTTGAGTTTGATCTATTAAGTCGTGCTTAGAATTTCAATCTCTAGCCTGC

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	53.60%	45.50%	0.87%	0.00%	NA
All Indica	2759	35.40%	63.40%	1.16%	0.00%	NA
All Japonica	1512	76.10%	23.50%	0.40%	0.00%	NA
Aus	269	98.50%	0.70%	0.74%	0.00%	NA
Indica I	595	18.70%	80.30%	1.01%	0.00%	NA
Indica II	465	48.80%	49.90%	1.29%	0.00%	NA
Indica III	913	41.80%	56.70%	1.42%	0.00%	NA
Indica Intermediate	786	32.70%	66.40%	0.89%	0.00%	NA
Temperate Japonica	767	97.70%	2.00%	0.39%	0.00%	NA
Tropical Japonica	504	35.50%	64.10%	0.40%	0.00%	NA
Japonica Intermediate	241	92.10%	7.50%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	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
vg0432568737	G -> A	LOC_Os04g54759.1	upstream_gene_variant ; 3332.0bp to feature; MODIFIER	silent_mutation	Average:28.46; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0432568737	G -> A	LOC_Os04g54780.1	upstream_gene_variant ; 1009.0bp to feature; MODIFIER	silent_mutation	Average:28.46; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0432568737	G -> A	LOC_Os04g54759-LOC_Os04g54780	intergenic_region ; MODIFIER	silent_mutation	Average:28.46; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432568737	NA	1.27E-07	mr1229	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
vg0432568737	NA	1.01E-09	mr1403	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
vg0432568737	1.38E-10	NA	mr1800_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
vg0432568737	3.04E-06	2.22E-06	mr1800_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
vg0432568737	1.19E-07	NA	mr1800_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