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Detailed information for vg0220780924:

Variant ID: vg0220780924 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20780924
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAAAAAATTGTCTCACCCCTCTCTTAATAAATTTCGATACGGGCCCCCTTCCTCTCATATCCAATGCCTAATTTCCCAACCACTAACCACACAAGCGC[G/A]
ACGTCTATCTCCTGATGTAATTCACACCTATGTATGTGACACCATTCCATTTACCTCCGGTTGCTGAACCTAACCGGAGGCAAAGAATATACTTCCTCCG

Reverse complement sequence

CGGAGGAAGTATATTCTTTGCCTCCGGTTAGGTTCAGCAACCGGAGGTAAATGGAATGGTGTCACATACATAGGTGTGAATTACATCAGGAGATAGACGT[C/T]
GCGCTTGTGTGGTTAGTGGTTGGGAAATTAGGCATTGGATATGAGAGGAAGGGGGCCCGTATCGAAATTTATTAAGAGAGGGGTGAGACAATTTTTTTTA

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	92.20%	4.40%	3.41%	0.00%	NA
All Indica	2759	87.50%	6.90%	5.69%	0.00%	NA
All Japonica	1512	99.40%	0.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	72.40%	10.10%	17.48%	0.00%	NA
Indica II	465	84.50%	12.70%	2.80%	0.00%	NA
Indica III	913	99.20%	0.40%	0.33%	0.00%	NA
Indica Intermediate	786	86.90%	8.40%	4.71%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	10.00%	3.33%	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
vg0220780924	G -> A	LOC_Os02g34640.1	downstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:54.833; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N
vg0220780924	G -> A	LOC_Os02g34650.1	downstream_gene_variant ; 1130.0bp to feature; MODIFIER	silent_mutation	Average:54.833; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N
vg0220780924	G -> A	LOC_Os02g34640-LOC_Os02g34650	intergenic_region ; MODIFIER	silent_mutation	Average:54.833; most accessible tissue: Minghui63 root, score: 78.091	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220780924	NA	4.49E-07	mr1358_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
vg0220780924	NA	4.68E-06	mr1550_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
vg0220780924	1.17E-06	NA	mr1717_2	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
vg0220780924	7.09E-06	NA	mr1770_2	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