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Detailed information for vg0107544024:

Variant ID: vg0107544024 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7544024
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TGATAAATACATCAAAACTTTTTATTGATAGTGAAATTATTGACTGCAAGTTTTTGCCAATAGTGAAATCATCGAAAGTGAAACCATTAGAAGCATTTAT[G/A]
AAATCATCGATAGGGAAAGGTTTGACAATAGTGAAATCATTTACGGTAAGTTTTTACCAAAGAACTTACATAAATGCTATAAGGGAAGAAAAAATGTGGT

Reverse complement sequence

ACCACATTTTTTCTTCCCTTATAGCATTTATGTAAGTTCTTTGGTAAAAACTTACCGTAAATGATTTCACTATTGTCAAACCTTTCCCTATCGATGATTT[C/T]
ATAAATGCTTCTAATGGTTTCACTTTCGATGATTTCACTATTGGCAAAAACTTGCAGTCAATAATTTCACTATCAATAAAAAGTTTTGATGTATTTATCA

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 96.20% 3.60% 0.25% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.50% 6.80% 0.73% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.10% 0.26% 0.00% NA
Tropical Japonica  504 82.10% 16.50% 1.39% 0.00% NA
Japonica Intermediate  241 91.30% 7.90% 0.83% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 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
vg0107544024 G -> A LOC_Os01g13510.1 missense_variant ; p.Met44Ile; MODERATE nonsynonymous_codon ; M44I Average:30.285; most accessible tissue: Callus, score: 55.379 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107544024 1.72E-06 1.72E-06 mr1098 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
vg0107544024 NA 6.41E-06 mr1101 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
vg0107544024 7.73E-08 7.73E-08 mr1589 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
vg0107544024 NA 1.31E-06 mr1961 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
vg0107544024 NA 1.83E-06 mr1098_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
vg0107544024 NA 6.44E-06 mr1150_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