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Detailed information for vg0434091958:

Variant ID: vg0434091958 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34091958
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TCGATCCCCTTTTCGATCTCTCAGCTGTCCTAATTCGCTCTCCTCAAAATGCCTCTTCTTCAGGACGAAGGCGATGGGTCGTTGCCGGTATGAGCCGTCA[C/A]
CGCGGAGGCTCTCGAGCTGCCGGCGAGGTGCGTACGGAGAGGGGAACGCGGGTGAGCGTTTCAGTTATTGTTCAATGTAGATGTGCAACTGAACTGCTTG

Reverse complement sequence

CAAGCAGTTCAGTTGCACATCTACATTGAACAATAACTGAAACGCTCACCCGCGTTCCCCTCTCCGTACGCACCTCGCCGGCAGCTCGAGAGCCTCCGCG[G/T]
TGACGGCTCATACCGGCAACGACCCATCGCCTTCGTCCTGAAGAAGAGGCATTTTGAGGAGAGCGAATTAGGACAGCTGAGAGATCGAAAAGGGGATCGA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.90% 12.70% 1.44% 0.00% NA
All Indica  2759 87.40% 10.90% 1.74% 0.00% NA
All Japonica  1512 88.00% 11.40% 0.60% 0.00% NA
Aus  269 66.20% 32.70% 1.12% 0.00% NA
Indica I  595 93.30% 4.00% 2.69% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 77.00% 22.10% 0.88% 0.00% NA
Indica Intermediate  786 88.50% 8.50% 2.93% 0.00% NA
Temperate Japonica  767 98.60% 0.90% 0.52% 0.00% NA
Tropical Japonica  504 69.00% 30.40% 0.60% 0.00% NA
Japonica Intermediate  241 94.20% 5.00% 0.83% 0.00% NA
VI/Aromatic  96 68.80% 28.10% 3.12% 0.00% NA
Intermediate  90 81.10% 13.30% 5.56% 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
vg0434091958 C -> A LOC_Os04g57230.1 missense_variant ; p.Pro48Thr; MODERATE nonsynonymous_codon ; P48T Average:89.605; most accessible tissue: Minghui63 flower, score: 92.871 benign 1.156 TOLERATED 0.41
vg0434091958 C -> A LOC_Os04g57230.2 missense_variant ; p.Pro48Thr; MODERATE nonsynonymous_codon ; P48T Average:89.605; most accessible tissue: Minghui63 flower, score: 92.871 benign 1.231 TOLERATED 0.42

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)
vg0434091958 C A -0.01 -0.01 -0.01 -0.02 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434091958 NA 2.63E-06 mr1040 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
vg0434091958 NA 3.61E-06 mr1206_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
vg0434091958 NA 6.69E-06 mr1236_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
vg0434091958 3.04E-06 3.04E-06 mr1455_2 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