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Detailed information for vg0416544450:

Variant ID: vg0416544450 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16544450
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:

TAATCATTTTTTAGCAATATTACAGAATCATTTAATCTATTAATTTCAGTCTCAGGAATATATTTGAAAGCTGCCAGCATTTGCTGTTAGGTTTTAGGCC[A/G]
CAGTTGGATGACGGCTTGATTTCCCTTTTACCATAGTTATGAATTTACGATTCCTGACTATTGTATCTAATCAATTGGGCTGCAGTCCTTTTATATCATC

Reverse complement sequence

GATGATATAAAAGGACTGCAGCCCAATTGATTAGATACAATAGTCAGGAATCGTAAATTCATAACTATGGTAAAAGGGAAATCAAGCCGTCATCCAACTG[T/C]
GGCCTAAAACCTAACAGCAAATGCTGGCAGCTTTCAAATATATTCCTGAGACTGAAATTAATAGATTAAATGATTCTGTAATATTGCTAAAAAATGATTA

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	63.80%	35.50%	0.15%	0.51%	NA
All Indica	2759	73.10%	26.40%	0.14%	0.43%	NA
All Japonica	1512	53.60%	45.80%	0.13%	0.53%	NA
Aus	269	48.30%	50.60%	0.37%	0.74%	NA
Indica I	595	57.00%	42.20%	0.17%	0.67%	NA
Indica II	465	77.00%	22.60%	0.00%	0.43%	NA
Indica III	913	79.50%	20.40%	0.00%	0.11%	NA
Indica Intermediate	786	75.40%	23.50%	0.38%	0.64%	NA
Temperate Japonica	767	39.50%	59.50%	0.26%	0.78%	NA
Tropical Japonica	504	71.60%	28.20%	0.00%	0.20%	NA
Japonica Intermediate	241	60.60%	39.00%	0.00%	0.41%	NA
VI/Aromatic	96	3.10%	94.80%	0.00%	2.08%	NA
Intermediate	90	64.40%	35.60%	0.00%	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
vg0416544450	A -> DEL	N	N	silent_mutation	Average:51.699; most accessible tissue: Callus, score: 80.204	N	N	N	N
vg0416544450	A -> G	LOC_Os04g28020.1	upstream_gene_variant ; 3849.0bp to feature; MODIFIER	silent_mutation	Average:51.699; most accessible tissue: Callus, score: 80.204	N	N	N	N
vg0416544450	A -> G	LOC_Os04g28010.1	downstream_gene_variant ; 1767.0bp to feature; MODIFIER	silent_mutation	Average:51.699; most accessible tissue: Callus, score: 80.204	N	N	N	N
vg0416544450	A -> G	LOC_Os04g28010.2	downstream_gene_variant ; 1767.0bp to feature; MODIFIER	silent_mutation	Average:51.699; most accessible tissue: Callus, score: 80.204	N	N	N	N
vg0416544450	A -> G	LOC_Os04g28010-LOC_Os04g28020	intergenic_region ; MODIFIER	silent_mutation	Average:51.699; most accessible tissue: Callus, score: 80.204	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416544450	NA	3.95E-06	mr1525_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
vg0416544450	NA	1.33E-06	mr1806_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