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Detailed information for vg0124416834:

Variant ID: vg0124416834 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24416834
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGACGGCAGGGCCATGGGCGGCGGTGGCAGGCCAATACCTGGTTGCGCATGGTAGCAGAGGTGGTCAGGAGAACAGCGCCGCGGCAGGTAGCAGCGAGC[T/C]
GTCGACGACGCCATGGCGGTGTTTCTTTGGGAGGCGGTGGGCGCTGCGGAGGACGTTGGCGGCAGGTGCGACGGAGGATGGTGGCGGCGGATGCGGCGGA

Reverse complement sequence

TCCGCCGCATCCGCCGCCACCATCCTCCGTCGCACCTGCCGCCAACGTCCTCCGCAGCGCCCACCGCCTCCCAAAGAAACACCGCCATGGCGTCGTCGAC[A/G]
GCTCGCTGCTACCTGCCGCGGCGCTGTTCTCCTGACCACCTCTGCTACCATGCGCAACCAGGTATTGGCCTGCCACCGCCGCCCATGGCCCTGCCGTCTC

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 78.30% 21.40% 0.15% 0.11% NA
All Indica  2759 99.60% 0.30% 0.04% 0.14% NA
All Japonica  1512 40.20% 59.60% 0.20% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.20% 0.00% 0.11% NA
Indica Intermediate  786 99.00% 0.60% 0.00% 0.38% NA
Temperate Japonica  767 19.00% 80.70% 0.26% 0.00% NA
Tropical Japonica  504 65.50% 34.50% 0.00% 0.00% NA
Japonica Intermediate  241 54.80% 44.80% 0.41% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 64.40% 31.10% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124416834 T -> DEL LOC_Os01g42909.1 N frameshift_variant Average:75.328; most accessible tissue: Minghui63 young leaf, score: 85.633 N N N N
vg0124416834 T -> C LOC_Os01g42909.1 synonymous_variant ; p.Thr5Thr; LOW synonymous_codon Average:75.328; most accessible tissue: Minghui63 young leaf, score: 85.633 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124416834 NA 3.78E-13 mr1035_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
vg0124416834 5.94E-07 NA mr1164_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
vg0124416834 NA 3.59E-06 mr1164_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
vg0124416834 NA 5.56E-09 mr1299_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
vg0124416834 NA 2.25E-11 mr1537_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
vg0124416834 NA 1.36E-06 mr1648_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
vg0124416834 NA 5.85E-10 mr1700_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
vg0124416834 NA 1.35E-06 mr1727_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
vg0124416834 NA 3.22E-11 mr1756_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
vg0124416834 NA 2.17E-07 mr1840_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
vg0124416834 3.77E-06 NA mr1851_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
vg0124416834 NA 2.81E-07 mr1856_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