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Detailed information for vg0222817936:

Variant ID: vg0222817936 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22817936
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TATCAGGCCTAGTACCTATAGGCCTCAAACCTAGTACCTAGGTATCAAACTTGGTATCCGTAAGTATTAGACCTAATATTTGTCATCTGATATCCACATG[T/C]
ATTATGGCTAGTGCCTGTAGGTATCAGGTATGGTGCCTGAGTATCAAACTCATCTAATACCCACATGTATCATGGATGATACATATAGGTATCAGGCCTA

Reverse complement sequence

TAGGCCTGATACCTATATGTATCATCCATGATACATGTGGGTATTAGATGAGTTTGATACTCAGGCACCATACCTGATACCTACAGGCACTAGCCATAAT[A/G]
CATGTGGATATCAGATGACAAATATTAGGTCTAATACTTACGGATACCAAGTTTGATACCTAGGTACTAGGTTTGAGGCCTATAGGTACTAGGCCTGATA

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 93.50% 1.90% 3.53% 1.14% NA
All Indica  2759 93.10% 3.20% 3.19% 0.54% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 57.60% 0.00% 28.25% 14.13% NA
Indica I  595 85.40% 8.60% 5.21% 0.84% NA
Indica II  465 96.10% 1.10% 1.72% 1.08% NA
Indica III  913 96.70% 1.20% 1.75% 0.33% NA
Indica Intermediate  786 92.90% 2.70% 4.20% 0.25% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 97.80% 0.00% 1.11% 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
vg0222817936 T -> DEL N N silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0222817936 T -> C LOC_Os02g37810.1 downstream_gene_variant ; 4190.0bp to feature; MODIFIER silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0222817936 T -> C LOC_Os02g37820.1 downstream_gene_variant ; 2490.0bp to feature; MODIFIER silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0222817936 T -> C LOC_Os02g37830.1 downstream_gene_variant ; 4128.0bp to feature; MODIFIER silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0222817936 T -> C LOC_Os02g37830.2 downstream_gene_variant ; 4128.0bp to feature; MODIFIER silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 N N N N
vg0222817936 T -> C LOC_Os02g37820-LOC_Os02g37830 intergenic_region ; MODIFIER silent_mutation Average:76.322; most accessible tissue: Minghui63 panicle, score: 91.227 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)
vg0222817936 T C -0.06 -0.06 -0.04 -0.03 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222817936 1.05E-07 2.99E-08 mr1172_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