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: Categorical prediction for APOGEE bootstrap (July 2015 release)
  73. APOGEE bootstrap mean probability: Probability of being a harmful variant according to the APOGEE July 2015 release. P if > 0.5
  74. SNPDryad score: higher scores associate to more pathogenic variants (PMID: 24389653)
  75. MutationTaster: categorical prediction (disease_causing, disease_causing_automatic, polymorphism) (PMID: 24681721).
  76. MutationTaster score: confidence score for the prediction.
  77. dbSNP id: dbSNP accession number, ver. 149.
  78. dbSNP ClinSig: clinical significance, ver. 149.
  79. Mitomap Dec2016 status: clinical status according to MITOMAP (accessed on December 2016).
  80. Mitomap Dec2016 disease: pathogenic condition according to MITOMAP (accessed on December 2016).
  81. Mitomap Dec2016 somatic occurrence: flagged if this is a cancer-associated variant according to MITOMAP (accessed on December 2016).
  82. COSMIC id: COSMIC ver. 79 accession number if this is a cancer-associated variant.