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Detailed information for vg0421456232:

Variant ID: vg0421456232 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 21456232
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TTATTGCTGACGTGGCGTTGCGTGCGATGGGGGAAGGGAAGGTGGTGGGGGCGGTTACCTGTCTGCGCACAAAAGGGAGTGAGAGGAGGCGAGATAGAGG[C/T]
GACACATTTGGGATTCTTTCCCAGATAAGGGAATTTCCCAACAGATTTTGAATGAAGCAAAAGGGCAAACTTGCATGTTTGAGTTATTTTCTTCGCAACC

Reverse complement sequence

GGTTGCGAAGAAAATAACTCAAACATGCAAGTTTGCCCTTTTGCTTCATTCAAAATCTGTTGGGAAATTCCCTTATCTGGGAAAGAATCCCAAATGTGTC[G/A]
CCTCTATCTCGCCTCCTCTCACTCCCTTTTGTGCGCAGACAGGTAACCGCCCCCACCACCTTCCCTTCCCCCATCGCACGCAACGCCACGTCAGCAATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.80% 18.90% 0.04% 0.21% NA
All Indica  2759 70.40% 29.30% 0.07% 0.18% NA
All Japonica  1512 99.80% 0.10% 0.00% 0.13% NA
Aus  269 73.60% 26.40% 0.00% 0.00% NA
Indica I  595 82.50% 17.30% 0.17% 0.00% NA
Indica II  465 76.60% 23.20% 0.00% 0.22% NA
Indica III  913 62.00% 38.00% 0.00% 0.00% NA
Indica Intermediate  786 67.40% 31.90% 0.13% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0421456232 C -> DEL N N silent_mutation Average:98.085; most accessible tissue: Zhenshan97 flower, score: 99.208 N N N N
vg0421456232 C -> T LOC_Os04g35280.1 upstream_gene_variant ; 192.0bp to feature; MODIFIER silent_mutation Average:98.085; most accessible tissue: Zhenshan97 flower, score: 99.208 N N N N
vg0421456232 C -> T LOC_Os04g35280-LOC_Os04g35290 intergenic_region ; MODIFIER silent_mutation Average:98.085; most accessible tissue: Zhenshan97 flower, score: 99.208 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)
vg0421456232 C T -0.03 -0.05 -0.06 0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0421456232 NA 1.91E-06 mr1066_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
vg0421456232 8.52E-06 6.01E-06 mr1267_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
vg0421456232 4.63E-06 4.63E-06 mr1267_2 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
vg0421456232 NA 1.74E-06 mr1272_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
vg0421456232 5.83E-06 NA mr1598_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
vg0421456232 4.95E-06 2.26E-09 mr1940_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
vg0421456232 NA 7.00E-06 mr1952_2 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