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Detailed information for vg0402458498:

Variant ID: vg0402458498 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2458498
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, C: 0.47, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTGCGATAGTTTTTTAGCAATTCCCTTTTTTTATCCACCCTTAGCCATGTACCTAGGTTTCTTTTATTAATAACATAAAATAAAATATATCAACTGTA[A/C]
CTTATAATTTTGCAAATATATGGACCAATGCCCATCACTAGCTCGTGGAAAATAAACGAAAAAGTTCAAAGGTGACAAGACATGCAATTATTGAAAAACA

Reverse complement sequence

TGTTTTTCAATAATTGCATGTCTTGTCACCTTTGAACTTTTTCGTTTATTTTCCACGAGCTAGTGATGGGCATTGGTCCATATATTTGCAAAATTATAAG[T/G]
TACAGTTGATATATTTTATTTTATGTTATTAATAAAAGAAACCTAGGTACATGGCTAAGGGTGGATAAAAAAAGGGAATTGCTAAAAAACTATCGCAAGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 32.80% 0.55% 0.00% NA
All Indica  2759 87.90% 12.00% 0.07% 0.00% NA
All Japonica  1512 23.10% 76.50% 0.40% 0.00% NA
Aus  269 94.10% 5.60% 0.37% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 77.20% 22.80% 0.00% 0.00% NA
Indica Intermediate  786 87.40% 12.30% 0.25% 0.00% NA
Temperate Japonica  767 4.20% 95.40% 0.39% 0.00% NA
Tropical Japonica  504 43.30% 56.30% 0.40% 0.00% NA
Japonica Intermediate  241 41.50% 58.10% 0.41% 0.00% NA
VI/Aromatic  96 67.70% 15.60% 16.67% 0.00% NA
Intermediate  90 64.40% 34.40% 1.11% 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
vg0402458498 A -> C LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:47.391; most accessible tissue: Callus, score: 76.934 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402458498 NA 3.91E-14 mr1010 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
vg0402458498 NA 9.30E-07 mr1037 Ind_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
vg0402458498 NA 1.18E-11 mr1069 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
vg0402458498 NA 4.30E-14 mr1149 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
vg0402458498 NA 3.35E-06 mr1576 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
vg0402458498 NA 1.06E-08 mr1637 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
vg0402458498 NA 1.88E-22 mr1689 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
vg0402458498 NA 6.18E-07 mr1690 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
vg0402458498 NA 1.57E-06 mr1729 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
vg0402458498 NA 3.66E-07 mr1785 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
vg0402458498 NA 4.06E-07 mr1804 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
vg0402458498 NA 3.75E-06 mr1837 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
vg0402458498 NA 5.77E-06 mr1689_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
vg0402458498 3.59E-10 NA mr1798_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
vg0402458498 9.17E-07 8.54E-10 mr1798_2 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
vg0402458498 NA 1.67E-07 mr1798_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
vg0402458498 NA 1.63E-07 mr1837_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