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Detailed information for vg0825346415:

Variant ID: vg0825346415 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25346415
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGAAAGGAGGAGAATTTGTTAGACGAATGTTGTAGAAATTTGACAACCATGAATGACTTAAACACAGTTCTACCAAGTGTTCAATTGTTAACTCTGTA[T/C]
GTTGCGTGGAAAGAAAGAGGTAAATATACCAACTGACATAATTCAATTTTGGGCTTATCCATTTCCTGAATCTAGGCACTATATAATTATTTGGTGAATT

Reverse complement sequence

AATTCACCAAATAATTATATAGTGCCTAGATTCAGGAAATGGATAAGCCCAAAATTGAATTATGTCAGTTGGTATATTTACCTCTTTCTTTCCACGCAAC[A/G]
TACAGAGTTAACAATTGAACACTTGGTAGAACTGTGTTTAAGTCATTCATGGTTGTCAAATTTCTACAACATTCGTCTAACAAATTCTCCTCCTTTCACT

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 80.90% 19.10% 0.00% 0.00% NA
All Indica  2759 77.30% 22.70% 0.00% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 7.10% 92.90% 0.00% 0.00% NA
Indica I  595 81.30% 18.70% 0.00% 0.00% NA
Indica II  465 90.80% 9.20% 0.00% 0.00% NA
Indica III  913 76.30% 23.70% 0.00% 0.00% NA
Indica Intermediate  786 67.60% 32.40% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0825346415 T -> C LOC_Os08g40020.1 3_prime_UTR_variant ; 140.0bp to feature; MODIFIER silent_mutation Average:41.207; most accessible tissue: Callus, score: 60.213 N N N N
vg0825346415 T -> C LOC_Os08g40010.1 downstream_gene_variant ; 2466.0bp to feature; MODIFIER silent_mutation Average:41.207; most accessible tissue: Callus, score: 60.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825346415 NA 4.03E-09 mr1587 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
vg0825346415 NA 1.50E-06 mr1665 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
vg0825346415 NA 2.62E-07 mr1582_2 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
vg0825346415 NA 5.30E-18 mr1587_2 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
vg0825346415 NA 8.32E-06 mr1965_2 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