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Detailed information for vg0408179042:

Variant ID: vg0408179042 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8179042
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTCTGGTTTGAGGGAGGAAATTCAGAACATTGTTGATTATAAGGAATTTAACTCTGTCAACAGTTGTTTCGGTTTGCTATGCTTGCAGAGAAGGAATT[A/G]
CAGGGGCGCGACCATCAGGGCAAGAGCAAGGCAAGCACATACACTCCGCGCACGACGCCATCTGCGGCACTGCCCAAGGCCGTCTCTTTTCGGGTGTCCT

Reverse complement sequence

AGGACACCCGAAAAGAGACGGCCTTGGGCAGTGCCGCAGATGGCGTCGTGCGCGGAGTGTATGTGCTTGCCTTGCTCTTGCCCTGATGGTCGCGCCCCTG[T/C]
AATTCCTTCTCTGCAAGCATAGCAAACCGAAACAACTGTTGACAGAGTTAAATTCCTTATAATCAACAATGTTCTGAATTTCCTCCCTCAAACCAGAATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 2.10% 3.64% 27.51% NA
All Indica  2759 56.10% 1.10% 0.80% 41.97% NA
All Japonica  1512 81.90% 3.80% 9.33% 4.89% NA
Aus  269 78.40% 0.40% 0.74% 20.45% NA
Indica I  595 48.40% 0.30% 0.34% 50.92% NA
Indica II  465 66.20% 2.20% 1.51% 30.11% NA
Indica III  913 56.30% 0.50% 0.77% 42.39% NA
Indica Intermediate  786 55.70% 1.80% 0.76% 41.73% NA
Temperate Japonica  767 97.80% 0.30% 0.65% 1.30% NA
Tropical Japonica  504 58.10% 9.50% 22.22% 10.12% NA
Japonica Intermediate  241 81.30% 3.30% 9.96% 5.39% NA
VI/Aromatic  96 84.40% 8.30% 5.21% 2.08% NA
Intermediate  90 83.30% 2.20% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408179042 A -> DEL LOC_Os04g14580.1 N frameshift_variant Average:13.776; most accessible tissue: Callus, score: 35.853 N N N N
vg0408179042 A -> G LOC_Os04g14580.1 synonymous_variant ; p.Leu211Leu; LOW synonymous_codon Average:13.776; most accessible tissue: Callus, score: 35.853 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408179042 NA 4.22E-06 mr1156 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
vg0408179042 3.56E-06 9.46E-17 mr1301 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
vg0408179042 NA 7.53E-09 mr1951 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
vg0408179042 4.88E-07 9.50E-11 mr1156_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
vg0408179042 NA 5.56E-06 mr1236_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
vg0408179042 NA 3.59E-16 mr1301_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
vg0408179042 NA 3.96E-06 mr1668_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