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Detailed information for vg0426438693:

Variant ID: vg0426438693 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 26438693
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


TAGCTAGTAAATTAACTGAAGTAGTAATTAATCTCCCCAAGAATCAATACCTAGTTAGATCGACAAAGCCATCGCATGAGTAAAAGAAAACATGAATACT[T/G]
CAAATCTTTTGAAGTCGAGTTCAACGAATATCTGACACACACAATCTTGGGAAGATACGAAATAAAGGGAATTGTACTGTGGTCACCCCAACAAGCTGAC

Reverse complement sequence

GTCAGCTTGTTGGGGTGACCACAGTACAATTCCCTTTATTTCGTATCTTCCCAAGATTGTGTGTGTCAGATATTCGTTGAACTCGACTTCAAAAGATTTG[A/C]
AGTATTCATGTTTTCTTTTACTCATGCGATGGCTTTGTCGATCTAACTAGGTATTGATTCTTGGGGAGATTAATTACTACTTCAGTTAATTTACTAGCTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.70% 0.15% 0.00% NA
All Indica  2759 99.30% 0.60% 0.04% 0.00% NA
All Japonica  1512 89.30% 10.30% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 98.20% 1.60% 0.26% 0.00% NA
Tropical Japonica  504 77.80% 21.80% 0.40% 0.00% NA
Japonica Intermediate  241 85.10% 14.10% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 0.00% 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
vg0426438693 T -> G LOC_Os04g44670.1 3_prime_UTR_variant ; 352.0bp to feature; MODIFIER silent_mutation Average:75.781; most accessible tissue: Minghui63 root, score: 91.22 N N N N
vg0426438693 T -> G LOC_Os04g44660.1 downstream_gene_variant ; 797.0bp to feature; MODIFIER silent_mutation Average:75.781; most accessible tissue: Minghui63 root, score: 91.22 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)
vg0426438693 T G -0.02 -0.01 0.0 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0426438693 NA 3.24E-06 mr1077_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
vg0426438693 NA 7.25E-06 mr1220_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
vg0426438693 NA 7.09E-06 mr1263_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
vg0426438693 NA 8.18E-06 mr1420_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
vg0426438693 3.27E-06 3.27E-06 mr1466_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
vg0426438693 NA 5.10E-06 mr1646_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
vg0426438693 NA 9.07E-06 mr1759_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
vg0426438693 NA 7.42E-06 mr1976_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