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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0825948078:

Variant ID: vg0825948078 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25948078
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.04, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTGCCATCGTCCTTGGTGATGATGATCGTTGCAGCCGGTGCCTGATTGCTCCCGTCGAGGAAGCCGGCCATCTGTGCGCCGCGCAGCGCGGCAAGAAC[T/C]
TGCGCCTTCCACAGCACGAAGTTGCTCTTGGTGAGCTTCTCAGAAACTGTCTGCCCATTGAGAGCAGATGGGTTGGAGGAAGAAGACGCCATTTGCGTCG

Reverse complement sequence

CGACGCAAATGGCGTCTTCTTCCTCCAACCCATCTGCTCTCAATGGGCAGACAGTTTCTGAGAAGCTCACCAAGAGCAACTTCGTGCTGTGGAAGGCGCA[A/G]
GTTCTTGCCGCGCTGCGCGGCGCACAGATGGCCGGCTTCCTCGACGGGAGCAATCAGGCACCGGCTGCAACGATCATCATCACCAAGGACGATGGCAAGA

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 45.70% 9.40% 1.33% 43.61% NA
All Indica  2759 18.00% 14.90% 1.96% 65.13% NA
All Japonica  1512 97.20% 0.10% 0.20% 2.45% NA
Aus  269 22.30% 7.10% 1.12% 69.52% NA
Indica I  595 6.20% 1.70% 1.18% 90.92% NA
Indica II  465 45.80% 21.10% 1.51% 31.61% NA
Indica III  913 6.20% 21.70% 2.30% 69.77% NA
Indica Intermediate  786 24.20% 13.40% 2.42% 60.05% NA
Temperate Japonica  767 97.80% 0.00% 0.00% 2.22% NA
Tropical Japonica  504 98.40% 0.20% 0.20% 1.19% NA
Japonica Intermediate  241 92.90% 0.40% 0.83% 5.81% NA
VI/Aromatic  96 83.30% 1.00% 2.08% 13.54% NA
Intermediate  90 58.90% 10.00% 1.11% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0825948078 T -> C LOC_Os08g41020.1 synonymous_variant ; p.Gln31Gln; LOW synonymous_codon Average:4.795; most accessible tissue: Callus, score: 8.079 N N N N
vg0825948078 T -> DEL LOC_Os08g41020.1 N frameshift_variant Average:4.795; most accessible tissue: Callus, score: 8.079 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0825948078 NA 1.02E-07 mr1045 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
vg0825948078 NA 3.37E-06 mr1064 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
vg0825948078 NA 2.83E-06 mr1122 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
vg0825948078 NA 4.23E-06 mr1377 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
vg0825948078 NA 3.46E-06 mr1637 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
vg0825948078 NA 3.32E-06 mr1745 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
vg0825948078 NA 9.50E-07 mr1830 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
vg0825948078 NA 8.92E-06 mr1974 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
vg0825948078 NA 1.94E-07 mr1325_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
vg0825948078 NA 1.09E-06 mr1326_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
vg0825948078 NA 4.38E-06 mr1745_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