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Detailed information for vg0406094634:

Variant ID: vg0406094634 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6094634
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGAGGGCCAGTGACGCGGCTGGCACTATTCGTCATCATCATGCGGTAGGGCCGTCGTTGTCTGGTAGTCTTCGTCGTCGTGGCCGACGCCCTCTGCCC[A/G]
AGCCGTCGCCGACCCATCCGCCTTGCGCCGCCGCCGACACCCATCCCCTCCATCGGATCTGGGTGGGGAAGGGTCGAGGGGAGGGGCAGTGACGCGGCCG

Reverse complement sequence

CGGCCGCGTCACTGCCCCTCCCCTCGACCCTTCCCCACCCAGATCCGATGGAGGGGATGGGTGTCGGCGGCGGCGCAAGGCGGATGGGTCGGCGACGGCT[T/C]
GGGCAGAGGGCGTCGGCCACGACGACGAAGACTACCAGACAACGACGGCCCTACCGCATGATGATGACGAATAGTGCCAGCCGCGTCACTGGCCCTCCCC

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	67.40%	11.50%	6.07%	15.02%	NA
All Indica	2759	54.40%	18.80%	8.12%	18.67%	NA
All Japonica	1512	97.30%	0.10%	0.46%	2.12%	NA
Aus	269	38.70%	1.10%	6.32%	53.90%	NA
Indica I	595	92.60%	2.50%	3.70%	1.18%	NA
Indica II	465	32.70%	21.10%	9.03%	37.20%	NA
Indica III	913	37.10%	32.30%	9.09%	21.47%	NA
Indica Intermediate	786	58.30%	14.20%	9.80%	17.68%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	94.20%	0.20%	0.79%	4.76%	NA
Japonica Intermediate	241	95.90%	0.40%	0.83%	2.90%	NA
VI/Aromatic	96	52.10%	14.60%	29.17%	4.17%	NA
Intermediate	90	65.60%	6.70%	12.22%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406094634	A -> DEL	N	N	silent_mutation	Average:70.062; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0406094634	A -> G	LOC_Os04g11195.1	downstream_gene_variant ; 1588.0bp to feature; MODIFIER	silent_mutation	Average:70.062; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0406094634	A -> G	LOC_Os04g11200.1	downstream_gene_variant ; 2581.0bp to feature; MODIFIER	silent_mutation	Average:70.062; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N
vg0406094634	A -> G	LOC_Os04g11180-LOC_Os04g11195	intergenic_region ; MODIFIER	silent_mutation	Average:70.062; most accessible tissue: Minghui63 flag leaf, score: 85.151	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406094634	9.81E-07	9.81E-07	mr1392	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