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Figure 4 | BMC Genomics

Figure 4

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

Figure 4

Frequency distribution for all final cluster (= variant) classifications. The cluster frequencies within their respective amplicons are indicated based on the final classification categories after the allele and artefact identification workflow. The frequencies on the x axis represent the proportion of reads within an amplicon (i.e. intra-amplicon frequency) that represent a given variant or cluster, while the y axis shows the total number of clusters over all amplicons for each intra-amplicon frequency range. The grey zone indicates the overlapping zone of artefacts and putative alleles, i.e. the zone between the most frequent variant classified as ‘putative artefact’ and the least frequent variant among the ‘putative alleles’ within an amplicon. The dotted line at 4.37% represents the threshold T2 according to Galan et al. [13] to separate putative alleles from putative artefacts. The most frequent artefact within an amplicon represented 5.4% of the total number of reads of this specific amplicon.

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