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Detailed information for vg0405053182:

Variant ID: vg0405053182 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5053182
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.17, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

CAATTCGTCGAAGGTTAATTCCAGGGTTCTAGTACCTCTAACCTTTGCCGTCCATATATACAGCTACAGATCATGTTGTTTTTGGTTCTGCGGTTTTGTC[G/A]
ATGGCGAGCGAGTTCGACATGTCCACATCTTGAGAGTCGAGACGGAGATAAATTAGCAGGATGATATTTACGAATATAAATCAGAAGCTTGCATCATGAG

Reverse complement sequence

CTCATGATGCAAGCTTCTGATTTATATTCGTAAATATCATCCTGCTAATTTATCTCCGTCTCGACTCTCAAGATGTGGACATGTCGAACTCGCTCGCCAT[C/T]
GACAAAACCGCAGAACCAAAAACAACATGATCTGTAGCTGTATATATGGACGGCAAAGGTTAGAGGTACTAGAACCCTGGAATTAACCTTCGACGAATTG

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	26.40%	6.90%	0.97%	65.72%	NA
All Indica	2759	4.80%	1.70%	1.20%	92.32%	NA
All Japonica	1512	70.90%	17.70%	0.26%	11.11%	NA
Aus	269	3.00%	1.90%	2.23%	92.94%	NA
Indica I	595	4.20%	0.00%	1.68%	94.12%	NA
Indica II	465	6.00%	5.20%	1.29%	87.53%	NA
Indica III	913	3.10%	1.00%	0.88%	95.07%	NA
Indica Intermediate	786	6.60%	1.70%	1.15%	90.59%	NA
Temperate Japonica	767	88.10%	10.70%	0.00%	1.17%	NA
Tropical Japonica	504	55.80%	15.10%	0.79%	28.37%	NA
Japonica Intermediate	241	47.70%	45.60%	0.00%	6.64%	NA
VI/Aromatic	96	8.30%	0.00%	1.04%	90.62%	NA
Intermediate	90	28.90%	8.90%	2.22%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405053182	G -> DEL	N	N	silent_mutation	Average:10.666; most accessible tissue: Callus, score: 56.775	N	N	N	N
vg0405053182	G -> A	LOC_Os04g09430-LOC_Os04g09450	intergenic_region ; MODIFIER	silent_mutation	Average:10.666; most accessible tissue: Callus, score: 56.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405053182	NA	1.89E-06	mr1569	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