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Detailed information for vg0824813029:

Variant ID: vg0824813029 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24813029
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGGCCGGATCCGCCTCTGTCCAAGATGGATCCGGCCTAGAGGAGGAAGTCCCGGCCGCCGAGATGACCATGGGCGCCGGACTGGAGCATGGCTATGG[G/C]
CGCGGCTTCCCTCCTCCCGCAACCGGCCAGGGGCGCGGCTGCCCGCCTCCTGCTGCCGGCCAGTGGCGCGGCCAGGGGCGCGGCTGCCCGCCTCCCGCTG

Reverse complement sequence

CAGCGGGAGGCGGGCAGCCGCGCCCCTGGCCGCGCCACTGGCCGGCAGCAGGAGGCGGGCAGCCGCGCCCCTGGCCGGTTGCGGGAGGAGGGAAGCCGCG[C/G]
CCATAGCCATGCTCCAGTCCGGCGCCCATGGTCATCTCGGCGGCCGGGACTTCCTCCTCTAGGCCGGATCCATCTTGGACAGAGGCGGATCCGGCCATCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.40% 13.10% 4.40% 1.06% NA
All Indica  2759 72.00% 21.70% 4.53% 1.78% NA
All Japonica  1512 94.90% 0.40% 4.63% 0.07% NA
Aus  269 96.70% 0.00% 3.35% 0.00% NA
Indica I  595 63.20% 30.10% 4.03% 2.69% NA
Indica II  465 46.20% 51.20% 2.58% 0.00% NA
Indica III  913 92.00% 0.00% 5.70% 2.30% NA
Indica Intermediate  786 70.70% 23.00% 4.71% 1.53% NA
Temperate Japonica  767 98.00% 0.40% 1.43% 0.13% NA
Tropical Japonica  504 93.10% 0.20% 6.75% 0.00% NA
Japonica Intermediate  241 88.80% 0.80% 10.37% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 80.00% 16.70% 3.33% 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
vg0824813029 G -> C LOC_Os08g39260.1 missense_variant ; p.Gly4Ala; MODERATE nonsynonymous_codon ; G4A Average:75.378; most accessible tissue: Zhenshan97 panicle, score: 93.133 unknown unknown TOLERATED 0.12
vg0824813029 G -> DEL LOC_Os08g39260.1 N frameshift_variant Average:75.378; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0824813029 G C 0.0 0.0 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824813029 9.21E-06 NA mr1127 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
vg0824813029 8.19E-06 8.19E-06 mr1516 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