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Detailed information for vg0224803179:

Variant ID: vg0224803179 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24803179
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGAGGAAAGGTGCATGCCTCGCTTCTAGCTCCAAGGAAGCTAGATCTGGGCAAGGTCCAGGAAGAGACTAAGGGCAAAGAGGTCAAAAAGAAATACGT[C/T]
GCTCCACAGGAGTTCCAACTAGGCATGCCATTGGTTGGAGATGACGTGCTTGCCGCAATGGGCACCGCTTGCAAGGACTTTCACTTATACTACATGGAGA

Reverse complement sequence

TCTCCATGTAGTATAAGTGAAAGTCCTTGCAAGCGGTGCCCATTGCGGCAAGCACGTCATCTCCAACCAATGGCATGCCTAGTTGGAACTCCTGTGGAGC[G/A]
ACGTATTTCTTTTTGACCTCTTTGCCCTTAGTCTCTTCCTGGACCTTGCCCAGATCTAGCTTCCTTGGAGCTAGAAGCGAGGCATGCACCTTTCCTCCCC

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 96.00% 0.20% 3.81% 0.00% NA
All Indica  2759 95.40% 0.30% 4.28% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 80.70% 0.00% 19.33% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 92.50% 0.60% 6.88% 0.00% NA
Indica III  913 92.90% 0.40% 6.68% 0.00% NA
Indica Intermediate  786 96.80% 0.10% 3.05% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 0.00% 7.29% 0.00% NA
Intermediate  90 96.70% 0.00% 3.33% 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
vg0224803179 C -> T LOC_Os02g40930.1 synonymous_variant ; p.Val427Val; LOW synonymous_codon Average:23.18; most accessible tissue: Zhenshan97 root, score: 32.766 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224803179 2.68E-06 2.90E-14 mr1498 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
vg0224803179 NA 1.47E-12 mr1769 Ind_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
vg0224803179 NA 1.65E-08 mr1925 Ind_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
vg0224803179 1.74E-06 8.29E-13 mr1951 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
vg0224803179 NA 6.93E-11 mr1498_2 Ind_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
vg0224803179 5.51E-06 1.27E-15 mr1769_2 Ind_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
vg0224803179 NA 1.12E-06 mr1925_2 Ind_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
vg0224803179 NA 1.55E-09 mr1951_2 Ind_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