CLC Genomics Workbench allows for two types of SNP reporting: Reporting of SNPs as annotations on the consensus sequence, or reporting of SNPs in a variant reporting table.

The SNP-annotations on the contig include this information:

• Reference symbol: The base found in the reference sequence. For contigs without a reference, it will be the base found in the consensus sequence.
• Allele variation: Displays which bases are found at this position.
• Variant frequency: The frequency of a given variant. If more variants are found, the frequency of each variant will be displayed.
• Coverage: The coverage at the SNP position.
• Position: The position relative to the consensus sequence (may be different than the reference sequence because of gaps).
• Overlapping annotations: This line shows if the SNP is covered by an annotation. For annotated reference sequences, this information can be used to tell if the SNP is found in e.g. a coding or non-coding region of the genome.

Screenshot 1: SNP annotation. Placing your mouse on the annotation will reveal additional information about the SNP.

The tabular SNP report shows all the SNPs found in the contig and includes the same type of information about each SNP. The table provides a valuable overview of the SNPs, whereas the annotations are useful for detailed inspection of a SNP, and also if the consensus sequence is used in further analysis in the CLC Genomics

Screenshot 2: A small part of a SNP variation table