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

BMC Bioinformatics

Table 1 Annotations by MToolBox pipeline

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

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

ISSN: 1471-2105