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Detailed information for vg0334422154:

Variant ID: vg0334422154 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34422154
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 35. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGAGAAAGTTCAATAGTATAGCCAACTACTAGCTCCAATTCATCTATAGCCAATCTAATAGCTCATTTATACAATAGTTATATAATACACTATTAATA[T/C]
CTAGTCTCACATGTCATAGATACACTGCGTCTTGGAGTCCGTGCTACAGCTGGATATAAATCTGTAGCCCGCTGCTATTCTCTCTCCTGATTTATATTTT

Reverse complement sequence

AAAATATAAATCAGGAGAGAGAATAGCAGCGGGCTACAGATTTATATCCAGCTGTAGCACGGACTCCAAGACGCAGTGTATCTATGACATGTGAGACTAG[A/G]
TATTAATAGTGTATTATATAACTATTGTATAAATGAGCTATTAGATTGGCTATAGATGAATTGGAGCTAGTAGTTGGCTATACTATTGAACTTTCTCTTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.30% 32.40% 8.15% 5.21% NA
All Indica  2759 25.30% 53.10% 13.23% 8.41% NA
All Japonica  1512 99.30% 0.50% 0.13% 0.07% NA
Aus  269 79.60% 13.40% 4.09% 2.97% NA
Indica I  595 8.70% 69.10% 18.99% 3.19% NA
Indica II  465 21.10% 51.80% 17.42% 9.68% NA
Indica III  913 33.20% 47.50% 7.23% 12.05% NA
Indica Intermediate  786 31.00% 48.20% 13.36% 7.38% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.40% 0.40% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 94.80% 1.00% 0.00% 4.17% NA
Intermediate  90 66.70% 24.40% 7.78% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0334422154 T -> C LOC_Os03g60560.1 upstream_gene_variant ; 2026.0bp to feature; MODIFIER silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 N N N N
vg0334422154 T -> C LOC_Os03g60550.1 downstream_gene_variant ; 2991.0bp to feature; MODIFIER silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 N N N N
vg0334422154 T -> C LOC_Os03g60550.2 downstream_gene_variant ; 2991.0bp to feature; MODIFIER silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 N N N N
vg0334422154 T -> C LOC_Os03g60550.3 downstream_gene_variant ; 2991.0bp to feature; MODIFIER silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 N N N N
vg0334422154 T -> C LOC_Os03g60550-LOC_Os03g60560 intergenic_region ; MODIFIER silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 N N N N
vg0334422154 T -> DEL N N silent_mutation Average:94.325; most accessible tissue: Minghui63 young leaf, score: 98.638 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)
vg0334422154 T C 0.01 0.0 0.02 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334422154 NA 3.87E-21 mr1051 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
vg0334422154 1.26E-07 NA mr1671 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
vg0334422154 1.12E-09 5.92E-09 mr1671 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
vg0334422154 NA 7.96E-07 mr1717 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
vg0334422154 NA 3.89E-10 mr1770 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
vg0334422154 NA 4.21E-07 mr1785 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
vg0334422154 1.89E-07 NA mr1671_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
vg0334422154 1.64E-08 5.67E-08 mr1671_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