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Detailed information for vg0413770697:

Variant ID: vg0413770697 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 13770697
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTTAATTGCAACGGACACAATGGTGTAATCGGATTATATATCGGATAAGTAATTTAAGAGAAAATTTTATAAGAAGAAAAAAAATATGCACAACCTAA[T/C]
AGCAAAAACTACTTGCATGCATGTCTGTAACGCTACTAGTACTTCTCACGTAATTGTCCGCGTCGCTCGTTAAGTCTAAATCGAGATGCCTCTCGAAATA

Reverse complement sequence

TATTTCGAGAGGCATCTCGATTTAGACTTAACGAGCGACGCGGACAATTACGTGAGAAGTACTAGTAGCGTTACAGACATGCATGCAAGTAGTTTTTGCT[A/G]
TTAGGTTGTGCATATTTTTTTTCTTCTTATAAAATTTTCTCTTAAATTACTTATCCGATATATAATCCGATTACACCATTGTGTCCGTTGCAATTAAATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.10% 10.70% 0.11% 0.00% NA
All Indica  2759 89.50% 10.50% 0.04% 0.00% NA
All Japonica  1512 91.10% 8.70% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.10% 10.80% 0.17% 0.00% NA
Indica II  465 79.80% 20.20% 0.00% 0.00% NA
Indica III  913 95.90% 4.10% 0.00% 0.00% NA
Indica Intermediate  786 88.00% 12.00% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 86.50% 13.50% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 21.20% 0.83% 0.00% NA
VI/Aromatic  96 24.00% 75.00% 1.04% 0.00% NA
Intermediate  90 82.20% 16.70% 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
vg0413770697 T -> C LOC_Os04g24100.1 upstream_gene_variant ; 4162.0bp to feature; MODIFIER silent_mutation Average:39.512; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N
vg0413770697 T -> C LOC_Os04g24110.1 upstream_gene_variant ; 624.0bp to feature; MODIFIER silent_mutation Average:39.512; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N
vg0413770697 T -> C LOC_Os04g24100-LOC_Os04g24110 intergenic_region ; MODIFIER silent_mutation Average:39.512; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0413770697 1.77E-06 NA mr1730 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
vg0413770697 5.78E-07 NA mr1350_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
vg0413770697 1.58E-08 2.61E-11 mr1350_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
vg0413770697 2.60E-07 NA mr1730_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
vg0413770697 4.07E-06 5.59E-07 mr1730_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