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Detailed information for vg0433924853:

Variant ID: vg0433924853 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33924853
Reference Allele: GAlternative Allele: T,A
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTAATCTATAATTAGCACATGTTTACTGTAGCAACATATAGGCTAATTATGAATTAATTAGGCTCAATAGATTCGTCTCGTAAATTAGTCTAGGGTTAT[G/T,A]
AAATGAGTTTTTATCATTAGTCTATATTTAATACTTCTAATTAGTGTCCAAACGTCTGATATGACAGGGACTAAAATCCAAACAAGGCCTTAGTCTCCTT

Reverse complement sequence

AAGGAGACTAAGGCCTTGTTTGGATTTTAGTCCCTGTCATATCAGACGTTTGGACACTAATTAGAAGTATTAAATATAGACTAATGATAAAAACTCATTT[C/A,T]
ATAACCCTAGACTAATTTACGAGACGAATCTATTGAGCCTAATTAATTCATAATTAGCCTATATGTTGCTACAGTAAACATGTGCTAATTATAGATTAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 1.90% 1.33% 0.00% A: 0.04%
All Indica  2759 99.90% 0.00% 0.00% 0.00% A: 0.07%
All Japonica  1512 90.50% 5.50% 4.03% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 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 99.80% 0.00% 0.00% 0.00% A: 0.22%
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 87.60% 6.80% 5.61% 0.00% NA
Tropical Japonica  504 98.60% 0.80% 0.60% 0.00% NA
Japonica Intermediate  241 82.60% 11.20% 6.22% 0.00% NA
VI/Aromatic  96 93.80% 5.20% 1.04% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0433924853 G -> A LOC_Os04g56900.1 upstream_gene_variant ; 698.0bp to feature; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N
vg0433924853 G -> A LOC_Os04g56910.1 downstream_gene_variant ; 3825.0bp to feature; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N
vg0433924853 G -> A LOC_Os04g56890-LOC_Os04g56900 intergenic_region ; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N
vg0433924853 G -> T LOC_Os04g56900.1 upstream_gene_variant ; 698.0bp to feature; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N
vg0433924853 G -> T LOC_Os04g56910.1 downstream_gene_variant ; 3825.0bp to feature; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N
vg0433924853 G -> T LOC_Os04g56890-LOC_Os04g56900 intergenic_region ; MODIFIER silent_mutation Average:39.505; most accessible tissue: Zhenshan97 root, score: 68.289 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433924853 1.25E-08 1.97E-09 mr1565 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
vg0433924853 NA 1.08E-06 mr1565_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