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Detailed information for vg1107474967:

Variant ID: vg1107474967 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7474967
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.25, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TATATGGTCCCACCTGTCATACATACATTGCGCCTTGAAGCCTATGCTGCAGCTGGCTACAGATCTATAGCCCGCTGCTCTTCTCTCTTATCTTTTATCT[T/C]
ATTAAAATATGTTTATAGCCAGCACTGTTAATGTTAATAGTGCTATTGTACATGCTCTAATTCATCCCTATAAAAGCTGAATTCTAAACGGCACCTTTAA

Reverse complement sequence

TTAAAGGTGCCGTTTAGAATTCAGCTTTTATAGGGATGAATTAGAGCATGTACAATAGCACTATTAACATTAACAGTGCTGGCTATAAACATATTTTAAT[A/G]
AGATAAAAGATAAGAGAGAAGAGCAGCGGGCTATAGATCTGTAGCCAGCTGCAGCATAGGCTTCAAGGCGCAATGTATGTATGACAGGTGGGACCATATA

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 36.60% 35.80% 0.55% 27.02% NA
All Indica  2759 20.60% 34.80% 0.58% 44.04% NA
All Japonica  1512 56.60% 40.50% 0.46% 2.38% NA
Aus  269 95.90% 2.20% 0.00% 1.86% NA
Indica I  595 22.70% 55.00% 0.84% 21.51% NA
Indica II  465 2.40% 31.80% 0.00% 65.81% NA
Indica III  913 26.40% 19.30% 0.55% 53.78% NA
Indica Intermediate  786 22.90% 39.40% 0.76% 36.90% NA
Temperate Japonica  767 55.90% 43.30% 0.39% 0.39% NA
Tropical Japonica  504 65.10% 32.70% 0.60% 1.59% NA
Japonica Intermediate  241 41.10% 48.10% 0.41% 10.37% NA
VI/Aromatic  96 27.10% 71.90% 1.04% 0.00% NA
Intermediate  90 25.60% 48.90% 2.22% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1107474967 T -> DEL N N silent_mutation Average:71.654; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg1107474967 T -> C LOC_Os11g13640.1 upstream_gene_variant ; 4085.0bp to feature; MODIFIER silent_mutation Average:71.654; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg1107474967 T -> C LOC_Os11g13650.1 upstream_gene_variant ; 770.0bp to feature; MODIFIER silent_mutation Average:71.654; most accessible tissue: Zhenshan97 panicle, score: 89.846 N N N N
vg1107474967 T -> C LOC_Os11g13650-LOC_Os11g13660 intergenic_region ; MODIFIER silent_mutation Average:71.654; most accessible tissue: Zhenshan97 panicle, score: 89.846 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)
vg1107474967 T C -0.02 -0.02 -0.01 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107474967 2.06E-06 NA mr1740 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