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Detailed information for vg0123089366:

Variant ID: vg0123089366 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23089366
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCCGGCGGGGATTTAGGCCGCAACGGCGGCATGATCAGATCCGTGCAGCCGCTGGGCTCGGAGGGTTCCCGAGATCCACCGCTAGGTTCATCCTCCCA[A/C]
GATGCCATCAGCCACGCCCCCACGCGACGCCGCCACTGCTTCCCTCGATCGACCGGCGCGCCGCCGCCGCCGCAATCGCCAGCGAGGGCAGCCGTCGAAA

Reverse complement sequence

TTTCGACGGCTGCCCTCGCTGGCGATTGCGGCGGCGGCGGCGCGCCGGTCGATCGAGGGAAGCAGTGGCGGCGTCGCGTGGGGGCGTGGCTGATGGCATC[T/G]
TGGGAGGATGAACCTAGCGGTGGATCTCGGGAACCCTCCGAGCCCAGCGGCTGCACGGATCTGATCATGCCGCCGTTGCGGCCTAAATCCCCGCCGGAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.80% 17.00% 0.17% 0.00% NA
All Indica  2759 96.30% 3.50% 0.18% 0.00% NA
All Japonica  1512 61.30% 38.60% 0.07% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 92.40% 7.10% 0.44% 0.00% NA
Indica Intermediate  786 97.10% 2.80% 0.13% 0.00% NA
Temperate Japonica  767 86.80% 13.20% 0.00% 0.00% NA
Tropical Japonica  504 30.80% 69.20% 0.00% 0.00% NA
Japonica Intermediate  241 44.00% 55.60% 0.41% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 72.20% 25.60% 2.22% 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
vg0123089366 A -> C LOC_Os01g40830.1 synonymous_variant ; p.Ser3Ser; LOW synonymous_codon Average:80.925; most accessible tissue: Zhenshan97 flower, score: 90.472 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)
vg0123089366 A C -0.01 0.0 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123089366 8.34E-07 NA mr1024_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
vg0123089366 NA 3.92E-07 mr1180_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
vg0123089366 NA 4.28E-07 mr1183_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
vg0123089366 NA 8.11E-06 mr1870_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