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Definitions of Discrepancy Types. |
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| Discrepancies defined on nucleotide and polypeptide levels |
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| Nucleotide changes |
Polypeptide changes |
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| Substitution |
Silent substitution |
| Conservative substitution |
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| Non-Conservative substitution |
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| Missense substitution – any amino acid change |
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| Truncation – inframe Stop codon |
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| Frameshift deletion |
Frameshift deletion |
| Frameshift insertion |
Frameshift insertion |
| Inframe deletion |
Inframe deletion |
| Inframe insertion |
Inframe insertion |
| No Stop codon |
Post-elongation |
| No Start codon |
No Translation |
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| Discrepancies defined on nucleotide level only |
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| Discrepancies introduced by sequence ambiguity |
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| Start codon substitution |
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| Stop codon substitution |
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| Substitution in CDS region |
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| Frameshift insertion |
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| Inframe insertion |
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| Discrepancies introduced by reference sequence ambiguity |
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| Substitution in CDS region |
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| Flanking sequence region (5' and 3' regions described separately) |
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| Substitution – replacement of one base by another |
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| Deletion/insertion – deletion/insertion of several bases |
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| Ambiguous substitution – replacement of a base by ambiguous base |
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| Ambiguous insertion – insertion of ambiguous base |
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| Discrepancy types for cDNA and flanking sequences defined at the nucleotide and polypeptide level by the Discrepancy Finder. |
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Taycher et al. BMC Bioinformatics 2007 8:198 doi:10.1186/1471-2105-8-198 |
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