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Detailed information for vg0142339408:

Variant ID: vg0142339408 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 42339408
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTTATGTACTTCAACGCAGCGAATGTATTTCAATGAATTTTGATATCAGCCTTTTATAATCCATTTGAAAACAAGAAAGAACTTGAATATTTCAACG[C/T]
TCGACAAAACTAATGCCCTGGACTTCTATTGAAAAAAAAAAGTACCAGGAACAACCTGCTCATCTTCTTCATCACAATAACCAAGCAATGAAACAAGGTT

Reverse complement sequence

AACCTTGTTTCATTGCTTGGTTATTGTGATGAAGAAGATGAGCAGGTTGTTCCTGGTACTTTTTTTTTTCAATAGAAGTCCAGGGCATTAGTTTTGTCGA[G/A]
CGTTGAAATATTCAAGTTCTTTCTTGTTTTCAAATGGATTATAAAAGGCTGATATCAAAATTCATTGAAATACATTCGCTGCGTTGAAGTACATAAATAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 9.00% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 73.50% 26.50% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 70.10% 29.90% 0.00% 0.00% NA
Tropical Japonica  504 72.40% 27.60% 0.00% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0142339408 C -> T LOC_Os01g72980.1 upstream_gene_variant ; 3654.0bp to feature; MODIFIER silent_mutation Average:36.696; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N
vg0142339408 C -> T LOC_Os01g72980.2 upstream_gene_variant ; 3654.0bp to feature; MODIFIER silent_mutation Average:36.696; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N
vg0142339408 C -> T LOC_Os01g72990.1 intron_variant ; MODIFIER silent_mutation Average:36.696; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N
vg0142339408 C -> T LOC_Os01g72990.2 intron_variant ; MODIFIER silent_mutation Average:36.696; most accessible tissue: Zhenshan97 young leaf, score: 57.159 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142339408 NA 2.81E-06 mr1028 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
vg0142339408 2.87E-07 NA mr1696 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