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Detailed information for vg0429999261:

Variant ID: vg0429999261 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29999261
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCCTTGGAACTTTAAGATTAGACCTTATAAATTTTGGAGTTAATTATCTAGTTGGCTTTCATTTTTATAATTGTTAGAAGTCTCGTCAAACGCTGCCA[C/T]
TTTACTCCTCTACGTCCCGTCCGCTGCCTCATCTATTTATTGTCATTAGGATTTTAAAAATCGAACATAATTATCGTCAGCGGCATTGCCATTATATTCC

Reverse complement sequence

GGAATATAATGGCAATGCCGCTGACGATAATTATGTTCGATTTTTAAAATCCTAATGACAATAAATAGATGAGGCAGCGGACGGGACGTAGAGGAGTAAA[G/A]
TGGCAGCGTTTGACGAGACTTCTAACAATTATAAAAATGAAAGCCAACTAGATAATTAACTCCAAAATTTATAAGGTCTAATCTTAAAGTTCCAAGGAGA

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 64.30% 35.10% 0.30% 0.28% NA
All Indica  2759 68.00% 31.00% 0.51% 0.47% NA
All Japonica  1512 56.70% 43.30% 0.00% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 80.20% 19.30% 0.34% 0.17% NA
Indica II  465 27.10% 71.60% 1.29% 0.00% NA
Indica III  913 79.30% 19.40% 0.33% 0.99% NA
Indica Intermediate  786 69.80% 29.40% 0.38% 0.38% NA
Temperate Japonica  767 91.10% 8.90% 0.00% 0.00% NA
Tropical Japonica  504 20.60% 79.40% 0.00% 0.00% NA
Japonica Intermediate  241 22.80% 77.20% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0429999261 C -> DEL N N silent_mutation Average:68.126; most accessible tissue: Callus, score: 80.018 N N N N
vg0429999261 C -> T LOC_Os04g50680.1 upstream_gene_variant ; 2000.0bp to feature; MODIFIER silent_mutation Average:68.126; most accessible tissue: Callus, score: 80.018 N N N N
vg0429999261 C -> T LOC_Os04g50690.1 upstream_gene_variant ; 502.0bp to feature; MODIFIER silent_mutation Average:68.126; most accessible tissue: Callus, score: 80.018 N N N N
vg0429999261 C -> T LOC_Os04g50700.1 upstream_gene_variant ; 2221.0bp to feature; MODIFIER silent_mutation Average:68.126; most accessible tissue: Callus, score: 80.018 N N N N
vg0429999261 C -> T LOC_Os04g50690-LOC_Os04g50700 intergenic_region ; MODIFIER silent_mutation Average:68.126; most accessible tissue: Callus, score: 80.018 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)
vg0429999261 C T -0.02 -0.02 -0.02 -0.03 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429999261 7.17E-06 3.98E-15 mr1169 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
vg0429999261 5.61E-07 4.15E-12 mr1169 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
vg0429999261 6.57E-11 4.62E-17 mr1174 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
vg0429999261 4.19E-14 2.40E-23 mr1174 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
vg0429999261 5.05E-09 2.87E-13 mr1347 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
vg0429999261 5.24E-08 1.27E-13 mr1347 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
vg0429999261 1.19E-07 7.78E-09 mr1406 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
vg0429999261 3.77E-06 9.85E-09 mr1406 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
vg0429999261 NA 3.76E-08 mr1042_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
vg0429999261 1.88E-09 3.88E-21 mr1174_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
vg0429999261 6.88E-15 3.70E-29 mr1174_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
vg0429999261 NA 3.93E-06 mr1246_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
vg0429999261 1.80E-12 1.46E-29 mr1347_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
vg0429999261 2.88E-15 5.82E-30 mr1347_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
vg0429999261 NA 3.75E-06 mr1354_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
vg0429999261 NA 4.17E-07 mr1404_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
vg0429999261 3.36E-06 2.88E-10 mr1406_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
vg0429999261 9.99E-07 3.27E-10 mr1406_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
vg0429999261 NA 2.36E-07 mr1680_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
vg0429999261 NA 9.48E-09 mr1871_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