Search for Variation information by Variation ID:

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

Detailed information for vg0520618572:

Variant ID: vg0520618572 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 20618572
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, A: 0.17, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

ACACCTTATGATCCTAGCTTGTTGCTTCGCAAGAACAAGAGAATTGCTAGGAATCAACTGGAATACTCCCAAATCATTGGCTTGCTGATGTACCTGGCTA[A/G]
TGCAACTAGGCCTGATATCTCCTTTGCTGTGAGCAAGTTGAGCCGGTTTACCTCTAATCCGGGAGATGATCACTGGCGTGCACTTGAGCGAGTAATGCGC

Reverse complement sequence

GCGCATTACTCGCTCAAGTGCACGCCAGTGATCATCTCCCGGATTAGAGGTAAACCGGCTCAACTTGCTCACAGCAAAGGAGATATCAGGCCTAGTTGCA[T/C]
TAGCCAGGTACATCAGCAAGCCAATGATTTGGGAGTATTCCAGTTGATTCCTAGCAATTCTCTTGTTCTTGCGAAGCAACAAGCTAGGATCATAAGGTGT

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	38.00%	20.30%	41.68%	0.00%	NA
All Indica	2759	14.30%	22.70%	63.03%	0.00%	NA
All Japonica	1512	81.20%	16.00%	2.78%	0.00%	NA
Aus	269	37.50%	15.20%	47.21%	0.00%	NA
Indica I	595	6.60%	23.90%	69.58%	0.00%	NA
Indica II	465	11.00%	32.90%	56.13%	0.00%	NA
Indica III	913	20.40%	19.40%	60.24%	0.00%	NA
Indica Intermediate	786	15.00%	19.60%	65.39%	0.00%	NA
Temperate Japonica	767	68.10%	27.20%	4.69%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	85.10%	13.30%	1.66%	0.00%	NA
VI/Aromatic	96	39.60%	30.20%	30.21%	0.00%	NA
Intermediate	90	41.10%	22.20%	36.67%	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
vg0520618572	A -> G	LOC_Os05g34750.1	missense_variant ; p.Asn876Ser; MODERATE	nonsynonymous_codon	Average:13.083; most accessible tissue: Minghui63 flower, score: 18.795	benign	-0.26	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0520618572	NA	6.03E-14	mr1062	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
vg0520618572	NA	2.65E-13	mr1905	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
vg0520618572	NA	1.40E-17	mr1913	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
vg0520618572	NA	2.86E-06	mr1913	Jap_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
vg0520618572	NA	2.17E-11	mr1938	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
vg0520618572	NA	5.65E-20	mr1062_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
vg0520618572	NA	4.33E-06	mr1062_2	Jap_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
vg0520618572	NA	1.04E-06	mr1321_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