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Detailed information for vg0202909303:

Variant ID: vg0202909303 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2909303
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGCTACTCTAAATCCATCCCTCAGTCAGTGCACTCCACCTAGTGCCATTCAACCACAAGCCATCATTGTTTGAACCCCTCCAATGAATGGTTTACCCC[A/G]
TCATGAACTAGGTTTGCAACACAATAACAGTTATGGTTCTGAAAATAGTGGTAACTTTTTTGGGGGAAAAAAAGAAAAGTATTATGAAAGACATGAGCGT

Reverse complement sequence

ACGCTCATGTCTTTCATAATACTTTTCTTTTTTTCCCCCAAAAAAGTTACCACTATTTTCAGAACCATAACTGTTATTGTGTTGCAAACCTAGTTCATGA[T/C]
GGGGTAAACCATTCATTGGAGGGGTTCAAACAATGATGGCTTGTGGTTGAATGGCACTAGGTGGAGTGCACTGACTGAGGGATGGATTTAGAGTAGCTGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.90% 20.00% 0.15% 0.00% NA
All Indica  2759 97.20% 2.70% 0.07% 0.00% NA
All Japonica  1512 58.40% 41.40% 0.20% 0.00% NA
Aus  269 17.10% 82.90% 0.00% 0.00% NA
Indica I  595 97.00% 2.70% 0.34% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 95.90% 4.10% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 43.30% 56.50% 0.26% 0.00% NA
Tropical Japonica  504 88.30% 11.70% 0.00% 0.00% NA
Japonica Intermediate  241 44.00% 55.60% 0.41% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 76.70% 21.10% 2.22% 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
vg0202909303 A -> G LOC_Os02g05880.1 intron_variant ; MODIFIER silent_mutation Average:50.56; most accessible tissue: Callus, score: 81.91 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202909303 NA 1.14E-07 mr1045 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
vg0202909303 NA 9.75E-12 mr1157 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
vg0202909303 NA 2.97E-08 mr1328 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
vg0202909303 NA 6.53E-13 mr1446 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
vg0202909303 NA 3.33E-14 mr1540 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
vg0202909303 NA 2.45E-14 mr1732 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
vg0202909303 NA 6.82E-11 mr1989 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