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Detailed information for vg0825510141:

Variant ID: vg0825510141 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25510141
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTAAGTGCGCCGTGCGCGGGAACACGCGCCGCCGCTGACGCCGCCGTCCCCCATCCACCAGAGCGCCGGCAGCCCGCTCGCCTTCCCCTCTTCCTCCT[C/T]
TCGGTTCTCTGTGAAACAGAGAGAAGAGAGAAGACGGGAGGAAGAAGGAGGAAAAGAAAAAGAAACGGAAAGGCTATATGACTGTCGCATGTTTTTGTTG

Reverse complement sequence

CAACAAAAACATGCGACAGTCATATAGCCTTTCCGTTTCTTTTTCTTTTCCTCCTTCTTCCTCCCGTCTTCTCTCTTCTCTCTGTTTCACAGAGAACCGA[G/A]
AGGAGGAAGAGGGGAAGGCGAGCGGGCTGCCGGCGCTCTGGTGGATGGGGGACGGCGGCGTCAGCGGCGGCGCGTGTTCCCGCGCACGGCGCACTTAGGA

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 45.60% 6.50% 12.19% 35.72% NA
All Indica  2759 19.90% 11.00% 14.14% 54.91% NA
All Japonica  1512 97.70% 0.00% 0.93% 1.39% NA
Aus  269 2.20% 0.00% 57.62% 40.15% NA
Indica I  595 42.90% 5.70% 7.23% 44.20% NA
Indica II  465 11.60% 21.10% 16.56% 50.75% NA
Indica III  913 10.20% 9.50% 17.85% 62.43% NA
Indica Intermediate  786 18.80% 10.80% 13.61% 56.74% NA
Temperate Japonica  767 98.00% 0.00% 0.26% 1.69% NA
Tropical Japonica  504 99.00% 0.00% 0.60% 0.40% NA
Japonica Intermediate  241 93.80% 0.00% 3.73% 2.49% NA
VI/Aromatic  96 81.20% 0.00% 8.33% 10.42% NA
Intermediate  90 50.00% 2.20% 10.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0825510141 C -> T LOC_Os08g40290.1 5_prime_UTR_variant ; 314.0bp to feature; MODIFIER silent_mutation Average:42.985; most accessible tissue: Zhenshan97 flower, score: 82.834 N N N N
vg0825510141 C -> DEL N N silent_mutation Average:42.985; most accessible tissue: Zhenshan97 flower, score: 82.834 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825510141 NA 1.12E-06 mr1728 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
vg0825510141 1.30E-06 NA mr1874 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
vg0825510141 1.30E-10 1.63E-15 mr1874 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
vg0825510141 NA 4.94E-09 mr1600_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
vg0825510141 NA 4.00E-10 mr1709_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
vg0825510141 NA 9.91E-08 mr1709_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
vg0825510141 2.92E-06 NA mr1874_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
vg0825510141 1.43E-08 3.18E-15 mr1874_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