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Detailed information for vg0417640422:

Variant ID: vg0417640422 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17640422
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, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCTCCCAGACTAACGGGAATAAGAAGGGCACATATATAGCACATGTTTTGTTCTCAAGAAGGAGAACAAACCTTGTACAAAATAGCAAATTAAATGAG[G/A]
CAAGCTGAACAAGTCAGTTATACATGACATATATATATATATATTGCAGGTTTTATTATTGTACCCTGTAACGTTTATGGGAAACAGGAGGAATCAAGAG

Reverse complement sequence

CTCTTGATTCCTCCTGTTTCCCATAAACGTTACAGGGTACAATAATAAAACCTGCAATATATATATATATATGTCATGTATAACTGACTTGTTCAGCTTG[C/T]
CTCATTTAATTTGCTATTTTGTACAAGGTTTGTTCTCCTTCTTGAGAACAAAACATGTGCTATATATGTGCCCTTCTTATTCCCGTTAGTCTGGGAGAAG

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	55.50%	22.30%	15.47%	6.71%	NA
All Indica	2759	32.20%	31.10%	25.30%	11.42%	NA
All Japonica	1512	98.10%	0.90%	0.93%	0.07%	NA
Aus	269	42.00%	55.80%	2.23%	0.00%	NA
Indica I	595	39.70%	46.60%	12.77%	1.01%	NA
Indica II	465	51.60%	7.30%	29.25%	11.83%	NA
Indica III	913	18.30%	32.20%	31.22%	18.29%	NA
Indica Intermediate	786	31.20%	32.20%	25.57%	11.07%	NA
Temperate Japonica	767	98.80%	0.10%	0.91%	0.13%	NA
Tropical Japonica	504	98.00%	1.20%	0.79%	0.00%	NA
Japonica Intermediate	241	95.90%	2.90%	1.24%	0.00%	NA
VI/Aromatic	96	81.20%	16.70%	2.08%	0.00%	NA
Intermediate	90	67.80%	18.90%	12.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0417640422	G -> DEL	N	N	silent_mutation	Average:38.874; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0417640422	G -> A	LOC_Os04g29630.1	upstream_gene_variant ; 1441.0bp to feature; MODIFIER	silent_mutation	Average:38.874; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0417640422	G -> A	LOC_Os04g29640.1	upstream_gene_variant ; 3054.0bp to feature; MODIFIER	silent_mutation	Average:38.874; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0417640422	G -> A	LOC_Os04g29650.1	upstream_gene_variant ; 4485.0bp to feature; MODIFIER	silent_mutation	Average:38.874; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0417640422	G -> A	LOC_Os04g29630-LOC_Os04g29640	intergenic_region ; MODIFIER	silent_mutation	Average:38.874; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417640422	NA	3.74E-06	mr1543_2	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