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Detailed information for vg0421119918:

Variant ID: vg0421119918 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21119918
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAATCCAAAAAAATTGTGGTATCCCTGTATACAGTAACCTCTGATTAACTCCCTGTATAATCTGACAATACTGAGGGACAAATGTAAGAGCATTTGCT[G/A]
GGATTTAATGAAATATTGGTTAGTTCTTGAGCTCGAATTGCTACCAAATCCCTAAACCCCTTTCTAAAATGCCACGGCACAGAGGTCATCACTGGCCTAC

Reverse complement sequence

GTAGGCCAGTGATGACCTCTGTGCCGTGGCATTTTAGAAAGGGGTTTAGGGATTTGGTAGCAATTCGAGCTCAAGAACTAACCAATATTTCATTAAATCC[C/T]
AGCAAATGCTCTTACATTTGTCCCTCAGTATTGTCAGATTATACAGGGAGTTAATCAGAGGTTACTGTATACAGGGATACCACAATTTTTTTGGATTTCA

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	95.40%	0.50%	1.48%	2.67%	NA
All Indica	2759	95.80%	0.60%	1.45%	2.14%	NA
All Japonica	1512	94.40%	0.20%	1.79%	3.64%	NA
Aus	269	97.40%	0.70%	0.74%	1.12%	NA
Indica I	595	95.80%	0.00%	1.85%	2.35%	NA
Indica II	465	90.50%	1.10%	3.01%	5.38%	NA
Indica III	913	98.70%	0.30%	0.11%	0.88%	NA
Indica Intermediate	786	95.50%	1.10%	1.78%	1.53%	NA
Temperate Japonica	767	98.30%	0.00%	0.26%	1.43%	NA
Tropical Japonica	504	87.50%	0.60%	4.96%	6.94%	NA
Japonica Intermediate	241	96.30%	0.00%	0.00%	3.73%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	94.40%	0.00%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0421119918	G -> DEL	N	N	silent_mutation	Average:12.787; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0421119918	G -> A	LOC_Os04g34830.1	upstream_gene_variant ; 3324.0bp to feature; MODIFIER	silent_mutation	Average:12.787; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0421119918	G -> A	LOC_Os04g36550.1	upstream_gene_variant ; 3619.0bp to feature; MODIFIER	silent_mutation	Average:12.787; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0421119918	G -> A	LOC_Os04g34840.1	upstream_gene_variant ; 3619.0bp to feature; MODIFIER	silent_mutation	Average:12.787; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N
vg0421119918	G -> A	LOC_Os04g34830-LOC_Os04g36550	intergenic_region ; MODIFIER	silent_mutation	Average:12.787; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421119918	1.46E-06	NA	mr1226_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
vg0421119918	3.24E-06	NA	mr1246_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