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Detailed information for vg0604025538:

Variant ID: vg0604025538 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4025538
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, A: 0.01, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGTTGTTTTATCACTCATAGTATTTTAAGTGTGATTTATATCTTATACATTTGCATAAAATTTTTGAATAAGACGAATGGTCAAACATGTGAGAAAAA[G/A]
TCAACGGCGTCATCTATTAAAAAACAGAGGGAGTATATCTACACAATTTGCAAATTTCAACTGAACACTTGTATATAGGGTATATATAGACATGCACAAA

Reverse complement sequence

TTTGTGCATGTCTATATATACCCTATATACAAGTGTTCAGTTGAAATTTGCAAATTGTGTAGATATACTCCCTCTGTTTTTTAATAGATGACGCCGTTGA[C/T]
TTTTTCTCACATGTTTGACCATTCGTCTTATTCAAAAATTTTATGCAAATGTATAAGATATAAATCACACTTAAAATACTATGAGTGATAAAACAACTCA

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	92.40%	7.30%	0.34%	0.00%	NA
All Indica	2759	91.80%	8.00%	0.18%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	53.50%	42.40%	4.09%	0.00%	NA
Indica I	595	80.00%	19.50%	0.50%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	97.90%	2.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.90%	10.80%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0604025538	G -> A	LOC_Os06g08300.2	downstream_gene_variant ; 2936.0bp to feature; MODIFIER	silent_mutation	Average:59.409; most accessible tissue: Callus, score: 82.512	N	N	N	N
vg0604025538	G -> A	LOC_Os06g08310.1	downstream_gene_variant ; 1823.0bp to feature; MODIFIER	silent_mutation	Average:59.409; most accessible tissue: Callus, score: 82.512	N	N	N	N
vg0604025538	G -> A	LOC_Os06g08300-LOC_Os06g08310	intergenic_region ; MODIFIER	silent_mutation	Average:59.409; most accessible tissue: Callus, score: 82.512	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604025538	NA	1.27E-07	mr1629	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
vg0604025538	NA	4.22E-06	mr1508_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