Table 1 Definition of terms used

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

1-2 bp diff

1-2 base pair (bp) differences to the most similar variant with a higher frequency within an amplicon

>2 bp diff

>2 bp differences to the most similar variant with a higher frequency within an amplicon