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Detailed information for vg0224747617:

Variant ID: vg0224747617 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 24747617
Reference Allele: AAGAlternative Allele: CAG,A
Primary Allele: AAGSecondary Allele: CAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTTTGGTCTACTGTTAATAAACCTCTGTCGGCACCAAACTGAGCAACCACTTCTTTTTGCCAAAGTTAAAGTGGAGTTTATCTGTTTTTGCCTTGAGC[AAG/CAG,A]
AGAGTACGGCTTTACACTTTGCATATGCGCGATAACTGATTGTAAAGTCTGTAACATCTTGGCTATAGGTTATGATGACGTGTTATGATCATATTGTTCT

Reverse complement sequence

AGAACAATATGATCATAACACGTCATCATAACCTATAGCCAAGATGTTACAGACTTTACAATCAGTTATCGCGCATATGCAAAGTGTAAAGCCGTACTCT[CTT/CTG,T]
GCTCAAGGCAAAAACAGATAAACTCCACTTTAACTTTGGCAAAAAGAAGTGGTTGCTCAGTTTGGTGCCGACAGAGGTTTATTAACAGTAGACCAAAATG

Allele Frequencies:

Populations Population SizeFrequency of AAG(primary allele) Frequency of CAG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 2.20% 0.15% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 93.00% 6.60% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 79.40% 19.40% 1.19% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg0224747617 AAG -> A LOC_Os02g40830.1 3_prime_UTR_variant ; 250.0bp to feature; MODIFIER N Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> A LOC_Os02g40830.2 3_prime_UTR_variant ; 250.0bp to feature; MODIFIER N Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> A LOC_Os02g40830.3 3_prime_UTR_variant ; 250.0bp to feature; MODIFIER N Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> A LOC_Os02g40840.1 downstream_gene_variant ; 1824.0bp to feature; MODIFIER N Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> CAG LOC_Os02g40830.1 3_prime_UTR_variant ; 245.0bp to feature; MODIFIER silent_mutation Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> CAG LOC_Os02g40830.2 3_prime_UTR_variant ; 245.0bp to feature; MODIFIER silent_mutation Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> CAG LOC_Os02g40830.3 3_prime_UTR_variant ; 245.0bp to feature; MODIFIER silent_mutation Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N
vg0224747617 AAG -> CAG LOC_Os02g40840.1 downstream_gene_variant ; 1825.0bp to feature; MODIFIER silent_mutation Average:80.063; most accessible tissue: Zhenshan97 root, score: 85.175 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224747617 2.84E-08 2.84E-08 mr1848 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