Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0416374336:

Variant ID: vg0416374336 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16374336
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTATTATTTTGCGAATATTAATTAGCTGTTTGATAGTACTCTATTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGACGAGGATTTAACACACAT[G/A]
TAAGCTTTTGGAATTTTTGATAGAAATTCTGGGCGTGACAAATTGGTATCAGAGCCACCTTGACCTTAGGACAAGTCAAATGGTAAATCTTAAGTAGCCT

Reverse complement sequence

AGGCTACTTAAGATTTACCATTTGACTTGTCCTAAGGTCAAGGTGGCTCTGATACCAATTTGTCACGCCCAGAATTTCTATCAAAAATTCCAAAAGCTTA[C/T]
ATGTGTGTTAAATCCTCGTCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAATAGAGTACTATCAAACAGCTAATTAATATTCGCAAAATAATAA

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	89.60%	10.40%	0.00%	0.00%	NA
All Indica	2759	98.30%	1.70%	0.00%	0.00%	NA
All Japonica	1512	72.20%	27.80%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	97.00%	3.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	69.00%	31.00%	0.00%	0.00%	NA
Tropical Japonica	504	71.60%	28.40%	0.00%	0.00%	NA
Japonica Intermediate	241	83.80%	16.20%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0416374336	G -> A	LOC_Os04g27700.1	upstream_gene_variant ; 1660.0bp to feature; MODIFIER	silent_mutation	Average:48.298; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N
vg0416374336	G -> A	LOC_Os04g27710.1	upstream_gene_variant ; 1190.0bp to feature; MODIFIER	silent_mutation	Average:48.298; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N
vg0416374336	G -> A	LOC_Os04g27690.1	downstream_gene_variant ; 2713.0bp to feature; MODIFIER	silent_mutation	Average:48.298; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N
vg0416374336	G -> A	LOC_Os04g27700-LOC_Os04g27710	intergenic_region ; MODIFIER	silent_mutation	Average:48.298; most accessible tissue: Minghui63 flag leaf, score: 63.692	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416374336	9.43E-06	NA	mr1057_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