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Detailed information for vg0434764872:

Variant ID: vg0434764872 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34764872
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.14, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCCCCGGGGGCCCCTTTTATATCACAGATGTGGAGGTCTCCTCATAGAACTCGGAGGTATCAGACCCTATACGATACGCCAACGACCCAGTTCTACCC[G/A]
AGTAGGATTCTTCCCATCTATAGATTCCGTGAAAGGTTTCCTTAGAATATACAGGAAATATCCGCATGCGCGTGGGTATGCCATATCGATATGTAACGTA

Reverse complement sequence

TACGTTACATATCGATATGGCATACCCACGCGCATGCGGATATTTCCTGTATATTCTAAGGAAACCTTTCACGGAATCTATAGATGGGAAGAATCCTACT[C/T]
GGGTAGAACTGGGTCGTTGGCGTATCGTATAGGGTCTGATACCTCCGAGTTCTATGAGGAGACCTCCACATCTGTGATATAAAAGGGGCCCCCGGGGGGG

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	57.40%	40.60%	1.97%	0.00%	NA
All Indica	2759	89.90%	7.10%	2.97%	0.00%	NA
All Japonica	1512	1.20%	98.70%	0.13%	0.00%	NA
Aus	269	52.00%	45.00%	2.97%	0.00%	NA
Indica I	595	92.40%	3.20%	4.37%	0.00%	NA
Indica II	465	91.80%	3.70%	4.52%	0.00%	NA
Indica III	913	89.70%	9.30%	0.99%	0.00%	NA
Indica Intermediate	786	87.00%	9.70%	3.31%	0.00%	NA
Temperate Japonica	767	0.30%	99.60%	0.13%	0.00%	NA
Tropical Japonica	504	2.40%	97.40%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	46.70%	52.20%	1.11%	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
vg0434764872	G -> A	LOC_Os04g58440.1	upstream_gene_variant ; 2449.0bp to feature; MODIFIER	silent_mutation	Average:40.51; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0434764872	G -> A	LOC_Os04g58420.1	downstream_gene_variant ; 1381.0bp to feature; MODIFIER	silent_mutation	Average:40.51; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0434764872	G -> A	LOC_Os04g58430.1	downstream_gene_variant ; 549.0bp to feature; MODIFIER	silent_mutation	Average:40.51; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0434764872	G -> A	LOC_Os04g58450.1	downstream_gene_variant ; 4160.0bp to feature; MODIFIER	silent_mutation	Average:40.51; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0434764872	G -> A	LOC_Os04g58420-LOC_Os04g58430	intergenic_region ; MODIFIER	silent_mutation	Average:40.51; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434764872	6.79E-07	6.79E-07	mr1447	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
vg0434764872	4.98E-06	4.98E-06	mr1454	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