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Detailed information for vg0404027324:

Variant ID: vg0404027324 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4027324
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGTGGAGGGGTAAACCGAGGTAGCGGCAGGGGAACTGTTTTATCATGCTTGGGAAATTCGCGAGAAGAGAAACGAGGTTTATTTCTTCACACCTGATC[G/A]
GGTAGATCTTTGTTTTGCTGACATTTGTGTGAAGACCCGAGACTTGTGCGAAAAAGACTAAGAGCTGCACAAGCATCGATAAATCAATAGGCTGAGGTTT

Reverse complement sequence

AAACCTCAGCCTATTGATTTATCGATGCTTGTGCAGCTCTTAGTCTTTTTCGCACAAGTCTCGGGTCTTCACACAAATGTCAGCAAAACAAAGATCTACC[C/T]
GATCAGGTGTGAAGAAATAAACCTCGTTTCTCTTCTCGCGAATTTCCCAAGCATGATAAAACAGTTCCCCTGCCGCTACCTCGGTTTACCCCTCCACTAC

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	51.00%	28.50%	0.47%	20.06%	NA
All Indica	2759	31.00%	39.10%	0.62%	29.29%	NA
All Japonica	1512	93.80%	1.70%	0.07%	4.37%	NA
Aus	269	27.90%	49.40%	1.49%	21.19%	NA
Indica I	595	53.60%	5.40%	0.50%	40.50%	NA
Indica II	465	37.40%	31.60%	0.65%	30.32%	NA
Indica III	913	12.80%	65.40%	0.55%	21.25%	NA
Indica Intermediate	786	31.30%	38.40%	0.76%	29.52%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	85.50%	3.60%	0.20%	10.71%	NA
Japonica Intermediate	241	92.90%	2.50%	0.00%	4.56%	NA
VI/Aromatic	96	11.50%	86.50%	0.00%	2.08%	NA
Intermediate	90	52.20%	31.10%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404027324	G -> DEL	N	N	silent_mutation	Average:32.905; most accessible tissue: Callus, score: 63.721	N	N	N	N
vg0404027324	G -> A	LOC_Os04g07570.1	downstream_gene_variant ; 1644.0bp to feature; MODIFIER	silent_mutation	Average:32.905; most accessible tissue: Callus, score: 63.721	N	N	N	N
vg0404027324	G -> A	LOC_Os04g07580.1	downstream_gene_variant ; 379.0bp to feature; MODIFIER	silent_mutation	Average:32.905; most accessible tissue: Callus, score: 63.721	N	N	N	N
vg0404027324	G -> A	LOC_Os04g07570-LOC_Os04g07580	intergenic_region ; MODIFIER	silent_mutation	Average:32.905; most accessible tissue: Callus, score: 63.721	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404027324	2.26E-07	6.39E-06	mr1035	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
vg0404027324	1.87E-06	NA	mr1626	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
vg0404027324	NA	6.13E-08	mr1915	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