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Table 1 Definition of terms used

From: MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

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
1-2 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