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Detailed information for vg0405900244:

Variant ID: vg0405900244 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5900244
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:


TACTCAAAATTTTATTAAACCTAGAAAGATAGTCATCCAAAGCTTCTCCAGGTTTCATCTCAAATTTAATATACTCCTTTTTGAAAAGATCACGACGAAG[C/T]
TCTTTAATATTATTTGTTCCTTGATGAAAATTATTCAAAGCAACCCAAATCTCATGAGCAGTTTGAAGATAAGCAACATGATCATAATCCGAACGAGAAA

Reverse complement sequence

TTTCTCGTTCGGATTATGATCATGTTGCTTATCTTCAAACTGCTCATGAGATTTGGGTTGCTTTGAATAATTTTCATCAAGGAACAAATAATATTAAAGA[G/A]
CTTCGTCGTGATCTTTTCAAAAAGGAGTATATTAAATTTGAGATGAAACCTGGAGAAGCTTTGGATGACTATCTTTCTAGGTTTAATAAAATTTTGAGTA

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 26.30% 17.60% 29.01% 27.06% NA
All Indica  2759 9.60% 20.90% 42.88% 26.60% NA
All Japonica  1512 60.30% 1.80% 7.21% 30.69% NA
Aus  269 9.30% 65.40% 11.15% 14.13% NA
Indica I  595 3.90% 14.60% 41.01% 40.50% NA
Indica II  465 14.00% 15.70% 38.06% 32.26% NA
Indica III  913 11.90% 26.70% 49.73% 11.61% NA
Indica Intermediate  786 8.80% 21.90% 39.19% 30.15% NA
Temperate Japonica  767 66.90% 0.50% 5.35% 27.25% NA
Tropical Japonica  504 43.70% 2.60% 9.52% 44.25% NA
Japonica Intermediate  241 74.30% 4.10% 8.30% 13.28% NA
VI/Aromatic  96 10.40% 40.60% 22.92% 26.04% NA
Intermediate  90 35.60% 14.40% 30.00% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0405900244 C -> DEL LOC_Os04g10880.1 N frameshift_variant Average:8.4; most accessible tissue: Callus, score: 20.87 N N N N
vg0405900244 C -> T LOC_Os04g10880.1 synonymous_variant ; p.Glu98Glu; LOW synonymous_codon Average:8.4; most accessible tissue: Callus, score: 20.87 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405900244 NA 1.36E-06 mr1114 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
vg0405900244 NA 7.92E-06 mr1116 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
vg0405900244 2.81E-06 2.27E-08 mr1117 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
vg0405900244 NA 1.39E-06 mr1240 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
vg0405900244 NA 6.38E-06 mr1247 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
vg0405900244 2.21E-06 2.21E-06 mr1266 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
vg0405900244 NA 6.72E-07 mr1496 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
vg0405900244 NA 5.99E-06 mr1682 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