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Detailed information for vg0804449148:

Variant ID: vg0804449148 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4449148
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAGCAGGGGTCATAAAAAGTGTGTTATGTGGGTCCCATAGAGAACCCTCTCAATCCTCTACTCCTTCCATTTTACCTGTGTTTGCTGTGGCTTTTGTT[A/G]
TGAGCTAGTGCCCACTGCTACACTGTTGGTGGCTACAAAGATGAATAGCAGCATTGATCCTAATAGTTGATATGCCCATGCAAAATATTATACTTGTCAT

Reverse complement sequence

ATGACAAGTATAATATTTTGCATGGGCATATCAACTATTAGGATCAATGCTGCTATTCATCTTTGTAGCCACCAACAGTGTAGCAGTGGGCACTAGCTCA[T/C]
AACAAAAGCCACAGCAAACACAGGTAAAATGGAAGGAGTAGAGGATTGAGAGGGTTCTCTATGGGACCCACATAACACACTTTTTATGACCCCTGCTAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	34.20%	4.40%	1.18%	60.18%	NA
All Indica	2759	4.40%	7.30%	1.74%	86.55%	NA
All Japonica	1512	95.00%	0.00%	0.00%	4.96%	NA
Aus	269	2.60%	1.10%	1.49%	94.80%	NA
Indica I	595	6.10%	2.20%	1.18%	90.59%	NA
Indica II	465	6.20%	8.20%	2.15%	83.44%	NA
Indica III	913	1.80%	10.80%	1.20%	86.20%	NA
Indica Intermediate	786	5.20%	6.50%	2.54%	85.75%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	88.70%	0.00%	0.00%	11.31%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	13.50%	0.00%	1.04%	85.42%	NA
Intermediate	90	41.10%	6.70%	3.33%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0804449148	A -> G	LOC_Os08g07890.1	downstream_gene_variant ; 957.0bp to feature; MODIFIER	silent_mutation	Average:16.529; most accessible tissue: Callus, score: 99.724	N	N	N	N
vg0804449148	A -> G	LOC_Os08g07890-LOC_Os08g07900	intergenic_region ; MODIFIER	silent_mutation	Average:16.529; most accessible tissue: Callus, score: 99.724	N	N	N	N
vg0804449148	A -> DEL	N	N	silent_mutation	Average:16.529; most accessible tissue: Callus, score: 99.724	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804449148	7.52E-06	7.51E-06	mr1664	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
vg0804449148	6.40E-06	6.40E-06	mr1664	Ind_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