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Detailed information for vg0513951648:

Variant ID: vg0513951648 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13951648
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAAAACCTTGAGCAACAAGTCTAGCTTTATTTCTCACAATCAAACCATCCTCATTTTGTTTATTTTTGAAAACCCACTTGGTTCCAATAATATTATGTC[T/C]
AGAAGGCGGTTCAACTAAAGTCCAAACTTTGTTCCTCTCAAAATTTTCATGTTCTTCATGCATGGCGTTAATCTACGATTCATCAGTTAATGCATGTGAC

Reverse complement sequence

GTCACATGCATTAACTGATGAATCGTAGATTAACGCCATGCATGAAGAACATGAAAATTTTGAGAGGAACAAAGTTTGGACTTTAGTTGAACCGCCTTCT[A/G]
GACATAATATTATTGGAACCAAGTGGGTTTTCAAAAATAAACAAAATGAGGATGGTTTGATTGTGAGAAATAAAGCTAGACTTGTTGCTCAAGGTTTTAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.20% 15.70% 0.11% 0.00% NA
All Indica  2759 98.80% 1.10% 0.11% 0.00% NA
All Japonica  1512 54.00% 46.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.60% 3.00% 0.34% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 21.30% 78.70% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 73.00% 27.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 2.22% 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
vg0513951648 T -> C LOC_Os05g24160.1 upstream_gene_variant ; 4976.0bp to feature; MODIFIER silent_mutation Average:16.373; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N
vg0513951648 T -> C LOC_Os05g24160.2 upstream_gene_variant ; 4976.0bp to feature; MODIFIER silent_mutation Average:16.373; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N
vg0513951648 T -> C LOC_Os05g24170.1 intron_variant ; MODIFIER silent_mutation Average:16.373; most accessible tissue: Zhenshan97 root, score: 29.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513951648 9.00E-07 NA mr1011 Ind_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
vg0513951648 NA 1.88E-08 mr1552 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
vg0513951648 NA 6.75E-08 mr1862 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
vg0513951648 NA 3.68E-07 mr1551_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