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Detailed information for vg0404380761:

Variant ID: vg0404380761 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4380761
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.52, A: 0.48, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CACGCTTAATATCAAAGTTCTTTGGAGATTGGCTTCCAAAAGAGTAGTTGTAGCTTGTTGGTATGAATATTCTATTAATCTTATTAAGCCCTAGGTCGGG[A/G]
TATGTCACACCCCAAAATCCTCCATTCATATACATTCATTTACATACACAACCATCAAAAATCATAAACAACAAAATTGTATAACTCATCGAGATCTACA

Reverse complement sequence

TGTAGATCTCGATGAGTTATACAATTTTGTTGTTTATGATTTTTGATGGTTGTGTATGTAAATGAATGTATATGAATGGAGGATTTTGGGGTGTGACATA[T/C]
CCCGACCTAGGGCTTAATAAGATTAATAGAATATTCATACCAACAAGCTACAACTACTCTTTTGGAAGCCAATCTCCAAAGAACTTTGATATTAAGCGTG

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	38.40%	18.90%	0.15%	42.62%	NA
All Indica	2759	58.40%	2.50%	0.18%	38.93%	NA
All Japonica	1512	4.20%	49.30%	0.13%	46.36%	NA
Aus	269	18.60%	20.80%	0.00%	60.59%	NA
Indica I	595	93.60%	0.80%	0.17%	5.38%	NA
Indica II	465	64.50%	3.70%	0.65%	31.18%	NA
Indica III	913	35.90%	1.50%	0.00%	62.54%	NA
Indica Intermediate	786	54.20%	4.20%	0.13%	41.48%	NA
Temperate Japonica	767	1.40%	86.70%	0.13%	11.73%	NA
Tropical Japonica	504	7.90%	6.00%	0.20%	85.91%	NA
Japonica Intermediate	241	5.40%	20.70%	0.00%	73.86%	NA
VI/Aromatic	96	49.00%	2.10%	0.00%	48.96%	NA
Intermediate	90	46.70%	21.10%	0.00%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404380761	A -> DEL	N	N	silent_mutation	Average:24.211; most accessible tissue: Callus, score: 48.672	N	N	N	N
vg0404380761	A -> G	LOC_Os04g08210-LOC_Os04g08230	intergenic_region ; MODIFIER	silent_mutation	Average:24.211; most accessible tissue: Callus, score: 48.672	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404380761	NA	5.59E-06	mr1037	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
vg0404380761	NA	7.50E-07	mr1037_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
vg0404380761	NA	1.38E-16	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
vg0404380761	NA	5.18E-06	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
vg0404380761	NA	4.26E-10	mr1798_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