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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1127363594:

Variant ID: vg1127363594 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27363594
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.69, T: 0.31, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


TCTATAGTCAATGTAATAGCCAATTCATACAATAGTTGCTTACTATACTATTAATATCTGGTCCCACATGTTATACACACATTACGTCTTAAAGTCTGTG[T/C]
TGCAGCTGTCTACAGATCTGTAACCCGTTGCTCTTTTCTCTCTTCCTTTACCTCTTTAAAATATGTTTATAGCTGGCTTAATTATAGTCTGCTATTGTAC

Reverse complement sequence

GTACAATAGCAGACTATAATTAAGCCAGCTATAAACATATTTTAAAGAGGTAAAGGAAGAGAGAAAAGAGCAACGGGTTACAGATCTGTAGACAGCTGCA[A/G]
CACAGACTTTAAGACGTAATGTGTGTATAACATGTGGGACCAGATATTAATAGTATAGTAAGCAACTATTGTATGAATTGGCTATTACATTGACTATAGA

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 43.50% 32.50% 1.65% 22.34% NA
All Indica  2759 53.10% 32.40% 1.12% 13.37% NA
All Japonica  1512 30.00% 31.40% 2.05% 36.57% NA
Aus  269 31.20% 25.70% 4.09% 39.03% NA
Indica I  595 44.90% 37.00% 0.84% 17.31% NA
Indica II  465 73.80% 22.20% 1.08% 3.01% NA
Indica III  913 45.20% 35.80% 1.42% 17.52% NA
Indica Intermediate  786 56.10% 31.20% 1.02% 11.70% NA
Temperate Japonica  767 51.90% 18.00% 1.69% 28.42% NA
Tropical Japonica  504 4.80% 44.80% 2.78% 47.62% NA
Japonica Intermediate  241 12.90% 46.10% 1.66% 39.42% NA
VI/Aromatic  96 18.80% 67.70% 1.04% 12.50% NA
Intermediate  90 40.00% 36.70% 4.44% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127363594 T -> DEL N N silent_mutation Average:49.092; most accessible tissue: Minghui63 root, score: 92.151 N N N N
vg1127363594 T -> C LOC_Os11g45200.1 upstream_gene_variant ; 2807.0bp to feature; MODIFIER silent_mutation Average:49.092; most accessible tissue: Minghui63 root, score: 92.151 N N N N
vg1127363594 T -> C LOC_Os11g45210.1 upstream_gene_variant ; 405.0bp to feature; MODIFIER silent_mutation Average:49.092; most accessible tissue: Minghui63 root, score: 92.151 N N N N
vg1127363594 T -> C LOC_Os11g45220.1 downstream_gene_variant ; 3131.0bp to feature; MODIFIER silent_mutation Average:49.092; most accessible tissue: Minghui63 root, score: 92.151 N N N N
vg1127363594 T -> C LOC_Os11g45210-LOC_Os11g45220 intergenic_region ; MODIFIER silent_mutation Average:49.092; most accessible tissue: Minghui63 root, score: 92.151 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)
vg1127363594 T C 0.04 -0.01 0.0 0.02 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127363594 NA 3.46E-08 mr1057 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
vg1127363594 3.12E-06 NA mr1276 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
vg1127363594 2.50E-06 2.50E-06 mr1276 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
vg1127363594 NA 1.61E-06 mr1652 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
vg1127363594 NA 2.69E-07 mr1057_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