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Detailed information for vg0403660277:

Variant ID: vg0403660277 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3660277
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: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAATCGATACCTATACTTTTCAACGAATCAAAAAAAAAAATCCCGCCTACCATCGCCGCCACTTTGCCACCTTATCCACCACCACCGCCGCCGTGGCC[G/A]
CCACCATCTCGCATGCCACGGTTGCTGCCCAATCCGCCATTAATTCCAATCGGCATCAGCTAGGCTACATACGTACGTGGTTAACGCAGTCCGATCTGTT

Reverse complement sequence

AACAGATCGGACTGCGTTAACCACGTACGTATGTAGCCTAGCTGATGCCGATTGGAATTAATGGCGGATTGGGCAGCAACCGTGGCATGCGAGATGGTGG[C/T]
GGCCACGGCGGCGGTGGTGGTGGATAAGGTGGCAAAGTGGCGGCGATGGTAGGCGGGATTTTTTTTTTTGATTCGTTGAAAAGTATAGGTATCGATTGGG

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	58.90%	27.10%	0.93%	13.01%	NA
All Indica	2759	48.20%	44.40%	0.76%	6.60%	NA
All Japonica	1512	76.30%	2.00%	0.79%	20.90%	NA
Aus	269	55.80%	0.00%	2.97%	41.26%	NA
Indica I	595	7.20%	90.90%	0.17%	1.68%	NA
Indica II	465	39.40%	48.40%	1.08%	11.18%	NA
Indica III	913	76.00%	17.70%	0.88%	5.37%	NA
Indica Intermediate	786	52.30%	37.80%	0.89%	9.03%	NA
Temperate Japonica	767	63.40%	0.80%	0.91%	34.94%	NA
Tropical Japonica	504	92.90%	4.00%	0.20%	2.98%	NA
Japonica Intermediate	241	83.00%	1.70%	1.66%	13.69%	NA
VI/Aromatic	96	95.80%	2.10%	1.04%	1.04%	NA
Intermediate	90	63.30%	28.90%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403660277	G -> DEL	N	N	silent_mutation	Average:46.801; most accessible tissue: Callus, score: 76.926	N	N	N	N
vg0403660277	G -> A	LOC_Os04g06920.1	upstream_gene_variant ; 2373.0bp to feature; MODIFIER	silent_mutation	Average:46.801; most accessible tissue: Callus, score: 76.926	N	N	N	N
vg0403660277	G -> A	LOC_Os04g06940.1	downstream_gene_variant ; 2621.0bp to feature; MODIFIER	silent_mutation	Average:46.801; most accessible tissue: Callus, score: 76.926	N	N	N	N
vg0403660277	G -> A	LOC_Os04g06920-LOC_Os04g06940	intergenic_region ; MODIFIER	silent_mutation	Average:46.801; most accessible tissue: Callus, score: 76.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403660277	NA	2.48E-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
vg0403660277	NA	8.54E-08	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
vg0403660277	1.25E-09	NA	mr1798_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
vg0403660277	5.46E-10	4.25E-13	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