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Table 1 Annotations by MToolBox pipeline

From: A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs

Variant annotation Status
Locus Previously provided
HF Previously provided
CI_lower;CI_upper Previously provided
RSRS Previously provided
MHCS Previously provided
rCRS Previously provided
Haplogroup Previously provided
Other Haplogroups Previously provided
Nt Variability Updated
Codon Position Previously provided
Aa Change Previously provided
Aa variability Updated
tRNA Annotation New
Disease Score Previously provided
RNA predictions New
MutPred Pred Previously provided
MutPred Prob Previously provided
PolyPhen-2 HumDiv Pred Previously provided
PolyPhen-2 HumDiv Prob Previously provided
PolyPhen-2 HumVar Pred Previously provided
PolyPhen-2 HumVar Prob Previously provided
PANTHER Pred Previously provided
PANTHER Prob Previously provided
PhD-SNP Pred Previously provided
PhD-SNP Prob Previously provided
SNPs&GO Pred Previously provided
SNPs&GO Prob Previously provided
MITOMAP Associated Disease(s) Updated
MITOMAP Homoplasmy Updated
MITOMAP Heteroplasmy Updated
Somatic Mutations Updated
SM Homoplasmy Updated
SM Heteroplasmy Updated
ClinVar New
OMIM Updated
dbSNP Updated
Mamit-tRNA Previously provided
PhastCons20Way New
PhyloP20Way New
AC/AN 1000 Genomes Previously provided
1000 Genomes Homoplasmy Previously provided
1000 Genomes Heteroplasmy Previously provided
  1. All the annotations provided by MToolBox pipeline are shown. In the latest update, new fields, mainly regarding tRNA gene variants, were added for a more accurate variant annotation in analyzed samples: structural information for tRNA variants (“tRNA annotation”), pathogenicity predictions for tRNA and rRNA genes (“RNA predictions”), disease reports in ClinVar database (“ClinVar”), conservation scores (“PhastCons20Way”, “PhyloP20Way”). tRNA annotation, in turn, includes five semi-colon separated annotations: position numbering in tRNA, tRNA type, cloverleaf secondary region, mature nucleotide and involvement of the specific position in tRNA folding (Y for yes or N for no). Moreover, data from HmtDB (“Nt variability”, “Aa variability”), MITOMAP (“MITOMAP Associated Disease(s)”, “MITOMAP Homoplasmy”, “MITOMAP Heteroplasmy”, “Somatic Mutations”, “SM Homoplasmy”, “SM Heteroplasmy”), OMIM links (“OMIM”) and dbSNP identifiers (“dbSNP”) were updated. All the remaining annotations were Previously provided by MToolBox