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Detailed information for vg0124680654:

Variant ID: vg0124680654 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24680654
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


GCATATATTTAGGGGGAGCAAATCCTATACATTTATTGTGCATGTTCTAGATCCATGTTGTTCACCTATTATTTATATCGGATCTTTGCACTTGAGCTTG[T/C]
ATACGAGTATATGACACTTGTGATGTTAATGAATACTCAACAAACATATCCATATCTTTCATATGCAACCAGTTGGTCATCAAGTGAAGGATGATAACCG

Reverse complement sequence

CGGTTATCATCCTTCACTTGATGACCAACTGGTTGCATATGAAAGATATGGATATGTTTGTTGAGTATTCATTAACATCACAAGTGTCATATACTCGTAT[A/G]
CAAGCTCAAGTGCAAAGATCCGATATAAATAATAGGTGAACAACATGGATCTAGAACATGCACAATAAATGTATAGGATTTGCTCCCCCTAAATATATGC

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 21.80% 0.30% 19.28% 58.61% NA
All Indica  2759 0.80% 0.00% 14.17% 84.99% NA
All Japonica  1512 61.00% 0.90% 20.44% 17.72% NA
Aus  269 1.10% 0.00% 61.71% 37.17% NA
Indica I  595 1.30% 0.00% 1.85% 96.81% NA
Indica II  465 0.20% 0.00% 5.59% 94.19% NA
Indica III  913 0.10% 0.00% 27.71% 72.18% NA
Indica Intermediate  786 1.70% 0.00% 12.85% 85.50% NA
Temperate Japonica  767 80.70% 0.80% 14.47% 4.04% NA
Tropical Japonica  504 25.80% 1.40% 33.53% 39.29% NA
Japonica Intermediate  241 71.80% 0.00% 12.03% 16.18% NA
VI/Aromatic  96 60.40% 0.00% 25.00% 14.58% NA
Intermediate  90 28.90% 0.00% 23.33% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124680654 T -> DEL N N silent_mutation Average:6.193; most accessible tissue: Callus, score: 15.203 N N N N
vg0124680654 T -> C LOC_Os01g43210.1 intron_variant ; MODIFIER silent_mutation Average:6.193; most accessible tissue: Callus, score: 15.203 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124680654 NA 7.92E-07 mr1388 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
vg0124680654 NA 7.82E-08 mr1757 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
vg0124680654 NA 4.43E-08 mr1045_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
vg0124680654 8.41E-07 NA mr1238_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
vg0124680654 NA 9.16E-07 mr1498_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
vg0124680654 NA 6.17E-06 mr1567_2 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
vg0124680654 NA 6.99E-07 mr1568_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
vg0124680654 3.34E-07 NA mr1733_2 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
vg0124680654 5.77E-07 NA mr1757_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
vg0124680654 NA 1.95E-06 mr1757_2 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
vg0124680654 5.37E-06 NA mr1841_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
vg0124680654 8.73E-07 NA mr1945_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