Legend of the output

  1. Chr: Genomic coordinate according to the Revised Cambridge Reference Sequence; Ncbi accession number: NC_012920.1
  2. Start: Genomic start position for the variant
  3. End: Genomic end position for the variant
  4. Ref: Reference nucleotide
  5. Alt: Alternative nucleotide
  6. MitImpact id: Accession number for the variant in MitImpact
  7. Gene symbol: Official gene symbol
  8. OXPHOS complex: Oxidative Phosphorylation Complex which the mitochondrial protein belongs to
  9. Ensembl gene id: Accession number in Ensembl Gene
  10. Ensembl protein id: Accession number in Ensembl Protein
  11. Ensembl transcript id: Accession number in Ensembl transcript
  12. Uniprot name: Gene symbol in Uniprot
  13. Uniprot id: Protein accession number in Uniprot
  14. NCBI gene id: Gene accession number for Ncbi
  15. NCBI protein id: Protein accession number for Ncbi
  16. Gene position: Variant position relative to the coordinate of the gene
  17. AA position: Amino acid position
  18. AA ref: Reference amino acid
  19. AA alt: Alternative amino acid
  20. Codon substitution: Codon substitution corresponding to the nucleotide change
  21. PhyloP 100V: PhyloP conservation index, from UCSC Table Browser 2015. See Pollard et at. 2010 for details.
  22. PhastCons 100V: PhastCons conservation index, from UCSC Table Browser 2015. See Pollard et at. 2010 for details.
  23. SiteVar: SiteVar conservation index, from Hmtdb 2014
  24. PolyPhen2: Categorical prediction for PolyPhen ver. 2.2.2 (HumDiv dataset). See Adzhubei et al. 2013 for details
  25. PolyPhen2 score: Score for PolyPhen ver. 2.2.2 (HumDiv dataset). See Adzhubei et al. 2013 for details
  26. SIFT: Categorical prediction for SIFT ver. 5.0.3. See Ng and Henikoff 2003 for details
  27. SIFT score: Score for SIFT ver. 5.0.3. See Ng and Henikoff 2003 for details
  28. FatHmm: Categorical prediction for FatHmm ver. 2.2 (unweighted version). See Shihab et al. 2013 for details.
  29. FatHmm score: Score for FatHmm ver. 2.2 (unweighted version). See Shihab et al. 2013 for details.
  30. FatHmmW: Categorical prediction for FatHmm ver. 2.3 (weighted version)
  31. FatHmmW score: Score for FatHmm ver. 2.3 (weighted version)
  32. PROVEAN: Categorical prediction for PROVEAN ver. 1.3. See Choi et al. 2012 for details
  33. PROVEAN score: Score for PROVEAN ver. 1.3. See Choi et al. 2012 for details
  34. MutationAssessor: Categorical prediction for MutationAssessor ver. 2.0. See Reva et al. 2011 for details
  35. MutationAssessor score: Score for MutationAssessor ver. 2.0. See Reva et al. 2011 for details
  36. EFIN SP: Categorical prediction for EFIN SP (trained with SwissProt dataset). See Zheng et al. 2014 for details
  37. EFIN SP score: Score for EFIN SP
  38. EFIN HD: Categorical prediction for EFIN HD (trained with HumDiv dataset)
  39. EFIN HD score: Score for EFIN HD
  40. CADD: Categorical prediction for CADD ver. 1.2
  41. CADD score: Score for CADD ver. 1.2. See Kircher et al. 2014 for details
  42. CADD phred: Phred-scaled score for CADD ver. 1.2
  43. VEST pvalue: Score-associated p-value (as computed by CRAVAT ver. 3.2). See Carter et al. 2013 for details
  44. VEST FDR: Score-associated False Discovery Rate
  45. PANTHER: Categorical prediction for PANTHER
  46. PANTHER score: Score (Thomas et al. 2003) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  47. PhD-SNP: Categorical prediction for PhD-SNP
  48. PhD-SNP score: Score for PhD-SNP (Capriotti et al. 2006) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  49. SNAP: Categorical prediction for SNAP
  50. SNAP score: Score for SNAP (Bromberg and Rost 2007) as computed by the Meta-SNP tool (Capriotti et al. 2013)
  51. Meta-SNP: Categorical prediction for
  52. Meta-SNP score: Consensus score for Meta-SNP (Capriotti et al. 2013)
  53. Meta-SNP RI: Meta-SNP score Reliability Index
  54. CAROL: Categorical prediction for CAROL consensus method. See Lopes et al. 2012 for details
  55. CAROL score: Score for CAROL consensus method
  56. Condel: Categorical prediction for Condel consensus method. See González-Pérez and López-Bigas 2011 for details
  57. Condel score: Score for Condel consensus method
  58. COVEC WMV: Categorical prediction for COVEC ver. 0.4 Weighted Majority Rule consensus method
  59. COVEC WMV score: Score for COVEC ver. 0.4 Weighted Majority Rule consensus method. See Frousios et al. 2013 for details
  60. MtoolBox: categorical prediction for MtoolBox consensus method
  61. MtoolBox DS: disease score for MtoolBox consensus method. See Santorsola et al. 2016 for details
  62. PolyPhen2 transf: Transformed PolyPhen2 categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  63. PolyPhen2 transf score: Transformed PolyPhen2 score
  64. SIFT transf: Transformed SIFT categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  65. SIFT transf score: Transformed SIFT score
  66. MutationAssessor transf: Transformed MutationAssessor categorical prediction by TransFIC ver. 1.0. See González-Pérez et al. 2013 for details
  67. MutationAssessor transf score: Transformed MutationAssessor score
  68. CHASM pvalue: CHASM score associated p-value (CRAVAT ver. 3.2). See Carter et al. 2009 for details
  69. CHASM FDR: CHASM score-associated False Discovery Rate
  70. MISTIC coevo sites: Proportion of significant coevolving sites for each amino acid site. Mutual information (MI) scores by MISTIC tool. See Simonetti et al. 2013 for details
  71. MISTIC mean MI score: Mean Mutual Information (MI) score for the amino acid site. See Simonetti et al. 2013 for details
  72. APOGEE bootstrap consensus: Consensus assessment of all categorical predictions obtained during the bootstrap loop (July 2015 release)
  73. APOGEE bootstrap mean probability (mp): Mean probability of being harmful over all bootstrap runs (July 2015 release).
  74. APOGEE bootstrap mp prediction: Categorical assessment inferred from the mp values obtained during all bootstrap runs. P if > 0.5
  75. SNPDryad score: higher scores associate to more pathogenic variants (PMID: 24389653)
  76. MutationTaster: categorical prediction (disease_causing, disease_causing_automatic, polymorphism) (PMID: 24681721).
  77. MutationTaster score: confidence score for the prediction.
  78. DEOGEN: DEOGEN functional score (see http://deogen2.mutaframe.com/ for details).
  79. dbSNP id: dbSNP accession number, ver. 150.
  80. dbSNP ClinSig: Variant's clinical significance, October 2017.
  81. dbSNP ClnDBN: Variant’s associated disease, October 2017.
  82. dbSNP ClnACC: Accession and version number assigned by ClinVar to the genotype/phenotype relationship, October 2017.
  83. dbSNP ClnDSDB: clinical significance, October 2017.
  84. Mitomap Dec2016 somatic occurrence: cancer-associated variant according to MITOMAP (accessed on December 2016).
  85. COSMIC id: COSMIC ver. 79 accession number if this is a cancer-associated variant.
  86. CPD candidate: Marked with 'CPD' if a human amino acid variant can be considered as a reliable “Compensated Pathogenic Deviations”. See Jordan et al.2015 (PMID:26123021), Azevedo et al. 2017 (PMID:27703146) for details.
  87. CPD frequency: Proportion of aligned orthologous sequences that carries a specific human pathogenic variant (homologous amino acid substitution). The total number of aligned orthologous sequences from mammalian reference mitochondrial genomes was 673 (for CYB, ND6), 674 (ND1, ND2, CO1, CO3), and 675 (all remaining genes) Sequences were downloaded from https://www.ncbi.nlm.nih.gov/genome/, October 2014). Frequencies have been calculated for all raw “CPDs” (column 85 represents a subset).
  88. Mitomap Allele: allele description for variants reported in Mitomap Database (accessed at July 2017, https://www.mitomap.org//foswiki/bin/view/MITOMAP/MutationsCodingControl).
  89. Mitomap Phenotype: Phenotypes associated to the Mitomap variant.
  90. Mitomap Homo: '+' indicates that the variant was found in homoplasmy.
  91. Mitomap Het: '-' indicates that the variant was found in heteroplasmy.
  92. Mitomap Status: Status of the Mitomap reported variants (see https://www.mitomap.org//foswiki/bin/view/MITOMAP/MutationsCodingControl for details).
  93. Mitomap NRef: Number of public references reporting a phenotype association.