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Detailed information for vg0433005106:

Variant ID: vg0433005106 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33005106
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATGTGGTAAGAATCGCATGATACTGGTTAGATATTAGGACCTGATACCAACCCAGTATCATCCCATTTTTGAACGAGATACTGGTATATAAAAACCCT[C/A]
AAAAAATAGTACAATTTGAGTTCCTCAACTATTTTTAGGTTGGATGTGATACGTGTCCTTCAATTGTAAAACTTAGGTATTTAATTACTCTATTAAAATC

Reverse complement sequence

GATTTTAATAGAGTAATTAAATACCTAAGTTTTACAATTGAAGGACACGTATCACATCCAACCTAAAAATAGTTGAGGAACTCAAATTGTACTATTTTTT[G/T]
AGGGTTTTTATATACCAGTATCTCGTTCAAAAATGGGATGATACTGGGTTGGTATCAGGTCCTAATATCTAACCAGTATCATGCGATTCTTACCACATGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 5.60% 0.06% 0.00% NA
All Indica  2759 98.60% 1.30% 0.11% 0.00% NA
All Japonica  1512 85.40% 14.60% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 97.10% 2.70% 0.17% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.40% 0.25% 0.00% NA
Temperate Japonica  767 82.00% 18.00% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0433005106 C -> A LOC_Os04g55500.1 upstream_gene_variant ; 1218.0bp to feature; MODIFIER silent_mutation Average:56.406; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0433005106 C -> A LOC_Os04g55490.1 downstream_gene_variant ; 2099.0bp to feature; MODIFIER silent_mutation Average:56.406; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N
vg0433005106 C -> A LOC_Os04g55490-LOC_Os04g55500 intergenic_region ; MODIFIER silent_mutation Average:56.406; most accessible tissue: Zhenshan97 panicle, score: 69.946 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433005106 9.71E-06 NA 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
vg0433005106 2.48E-06 NA mr1336 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