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Detailed information for vg0431498426:

Variant ID: vg0431498426 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31498426
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, A: 0.05, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CAGTGAGACATCCCCTTTATTTTTTCCCCCTCTTTTTTAAAAAGGAAAGAAACAAAATCCACGGAATAATTTCGTACGAGCCCGTGAGGCGCCGAGATTT[C/A]
TTTGCTCCGTGCAGCGCGAAATTCCCGGCTTCAGAATCATTCTGTCTTGTGCGGCCATCTCGTAATTTAAATTTTGACCGCTTTTCCTCCTGAAAATACC

Reverse complement sequence

GGTATTTTCAGGAGGAAAAGCGGTCAAAATTTAAATTACGAGATGGCCGCACAAGACAGAATGATTCTGAAGCCGGGAATTTCGCGCTGCACGGAGCAAA[G/T]
AAATCTCGGCGCCTCACGGGCTCGTACGAAATTATTCCGTGGATTTTGTTTCTTTCCTTTTTAAAAAAGAGGGGGAAAAAATAAAGGGGATGTCTCACTG

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 69.50% 30.20% 0.25% 0.00% NA
All Indica  2759 57.50% 42.10% 0.40% 0.00% NA
All Japonica  1512 87.00% 13.00% 0.00% 0.00% NA
Aus  269 84.80% 15.20% 0.00% 0.00% NA
Indica I  595 36.60% 62.70% 0.67% 0.00% NA
Indica II  465 52.50% 47.50% 0.00% 0.00% NA
Indica III  913 72.30% 27.50% 0.22% 0.00% NA
Indica Intermediate  786 59.00% 40.30% 0.64% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 69.20% 30.80% 0.00% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 1.11% 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
vg0431498426 C -> A LOC_Os04g52880.1 downstream_gene_variant ; 4263.0bp to feature; MODIFIER silent_mutation Average:81.514; most accessible tissue: Callus, score: 96.535 N N N N
vg0431498426 C -> A LOC_Os04g52900.1 downstream_gene_variant ; 4514.0bp to feature; MODIFIER silent_mutation Average:81.514; most accessible tissue: Callus, score: 96.535 N N N N
vg0431498426 C -> A LOC_Os04g52900.2 downstream_gene_variant ; 4514.0bp to feature; MODIFIER silent_mutation Average:81.514; most accessible tissue: Callus, score: 96.535 N N N N
vg0431498426 C -> A LOC_Os04g52890.1 intron_variant ; MODIFIER silent_mutation Average:81.514; most accessible tissue: Callus, score: 96.535 N N N N
vg0431498426 C -> A LOC_Os04g52890.2 intron_variant ; MODIFIER silent_mutation Average:81.514; most accessible tissue: Callus, score: 96.535 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)
vg0431498426 C A -0.03 -0.02 -0.05 -0.07 -0.07 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431498426 NA 2.56E-07 mr1233 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
vg0431498426 NA 1.52E-06 mr1248_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
vg0431498426 NA 1.69E-06 mr1252_2 Jap_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
vg0431498426 NA 2.22E-06 mr1255_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
vg0431498426 1.40E-06 2.92E-10 mr1800_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