Term used | Definition |
---|---|
Reads | Sequences passing quality filtering criteria according to the standard amplicon pipeline from Genome Sequencer FLX System Software |
Cluster | Set of identical reads within an amplicon |
Variant | Specific sequence of a cluster |
Putative artefact | Sequences or variants that are believed to result from polymerase or sequencing errors |
Chimera | Reads containing sequence motifs from two different putative alleles |
Putative allele | Variants that are believed to represent true alleles at the end of the allele and artefact identification workflow (Figure 2) |
Amplification efficiency | Relative frequency at which an allele is amplified for a given primer pair |
Allelic dropout | Alleles that are not detected in individuals that biologically possess those alleles |
1-2Â bp diff | 1-2 base pair (bp) differences to the most similar variant with a higher frequency within an amplicon |
>2Â bp diff | >2Â bp differences to the most similar variant with a higher frequency within an amplicon |