Search for Variation information by Variation ID:

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

Detailed information for vg0227036650:

Variant ID: vg0227036650 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27036650
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCGACACTCGCCCACCAAGAATACAACAGAATACTATCGACGTTTGATGTCTCGACTACGGTATTTGCATGGCATAGGGATCGTTGGTACTAGGATATAC[G/A]
CGAGACTGAGGTAAAAGAGACGGAGACATCGATTTTTATACAGGTTCAGGCCCTTGAATTGTCATGTAATAACCCTACATCCTGTTGGCCGAAGCCGGTC

Reverse complement sequence

GACCGGCTTCGGCCAACAGGATGTAGGGTTATTACATGACAATTCAAGGGCCTGAACCTGTATAAAAATCGATGTCTCCGTCTCTTTTACCTCAGTCTCG[C/T]
GTATATCCTAGTACCAACGATCCCTATGCCATGCAAATACCGTAGTCGAGACATCAAACGTCGATAGTATTCTGTTGTATTCTTGGTGGGCGAGTGTCGG

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	61.40%	38.00%	0.59%	0.00%	NA
All Indica	2759	88.60%	11.30%	0.07%	0.00%	NA
All Japonica	1512	10.30%	88.00%	1.72%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	91.10%	8.70%	0.17%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	79.30%	20.70%	0.00%	0.00%	NA
Indica Intermediate	786	91.70%	8.10%	0.13%	0.00%	NA
Temperate Japonica	767	17.70%	79.30%	3.00%	0.00%	NA
Tropical Japonica	504	3.20%	96.60%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	97.50%	0.83%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	40.00%	60.00%	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
vg0227036650	G -> A	LOC_Os02g44620.1	upstream_gene_variant ; 1818.0bp to feature; MODIFIER	silent_mutation	Average:74.353; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0227036650	G -> A	LOC_Os02g44610.1	downstream_gene_variant ; 907.0bp to feature; MODIFIER	silent_mutation	Average:74.353; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0227036650	G -> A	LOC_Os02g44610-LOC_Os02g44620	intergenic_region ; MODIFIER	silent_mutation	Average:74.353; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227036650	NA	2.37E-06	Awn_length	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0227036650	NA	5.97E-11	mr1070	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
vg0227036650	NA	2.65E-09	mr1097	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
vg0227036650	NA	2.03E-07	mr1604	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
vg0227036650	NA	2.91E-06	mr1332_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
vg0227036650	NA	6.61E-19	mr1336_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
vg0227036650	NA	2.48E-07	mr1380_2	Jap_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
vg0227036650	2.55E-06	2.55E-06	mr1499_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
vg0227036650	NA	1.08E-06	mr1561_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
vg0227036650	NA	5.50E-06	mr1576_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
vg0227036650	NA	1.68E-14	mr1579_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
vg0227036650	NA	1.05E-06	mr1627_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
vg0227036650	3.52E-06	3.52E-06	mr1908_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
vg0227036650	NA	6.43E-06	mr1977_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