Search for Variation information by Variation ID:

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

Detailed information for vg0520840504:

Variant ID: vg0520840504 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20840504
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.22, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCATTTGGGACATCCGTGGACATTGTCACACGATTCTTGAACCATTCGTTGAACCGAGAATTATGTTCTCTGTTAATCCATGCATCAGATCGCCCCAA[A/G]
TTCTCATCTCGGATTTTCGCTAAGTACTCCTCAAAGTATGGGCCAACTTCTGCCATATGTTGGAGCACAGCGTAATGAGCCTGCGTGTACGACGCTTGAT

Reverse complement sequence

ATCAAGCGTCGTACACGCAGGCTCATTACGCTGTGCTCCAACATATGGCAGAAGTTGGCCCATACTTTGAGGAGTACTTAGCGAAAATCCGAGATGAGAA[T/C]
TTGGGGCGATCTGATGCATGGATTAACAGAGAACATAATTCTCGGTTCAACGAATGGTTCAAGAATCGTGTGACAATGTCCACGGATGTCCCAAATGAGA

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	40.60%	0.10%	7.22%	52.12%	NA
All Indica	2759	8.80%	0.20%	6.89%	84.12%	NA
All Japonica	1512	97.90%	0.00%	0.07%	1.98%	NA
Aus	269	22.30%	0.00%	52.42%	25.28%	NA
Indica I	595	13.60%	0.50%	4.71%	81.18%	NA
Indica II	465	8.00%	0.00%	5.59%	86.45%	NA
Indica III	913	5.00%	0.00%	8.76%	86.20%	NA
Indica Intermediate	786	10.10%	0.30%	7.12%	82.57%	NA
Temperate Japonica	767	96.60%	0.00%	0.13%	3.26%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	0.00%	2.08%	2.08%	NA
Intermediate	90	45.60%	0.00%	7.78%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0520840504	A -> DEL	LOC_Os05g35100.1	N	frameshift_variant	Average:17.576; most accessible tissue: Callus, score: 30.874	N	N	N	N
vg0520840504	A -> G	LOC_Os05g35100.1	synonymous_variant ; p.Asn719Asn; LOW	synonymous_codon	Average:17.576; most accessible tissue: Callus, score: 30.874	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520840504	5.44E-07	NA	mr1907	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