UDPS data treatment workflow to obtain error-free HCV haplotypes as a sampling of the actual HCV viral quasispecies.

<p>UDPS data treatment workflow to obtain error-free HCV haplotypes as a sampling of the actual HCV viral quasispecies.</p

Reproducibility: Comparison of mutant abundance at each polymorphic site for a single amplicon replicated on three platforms, located in two laboratories when considering all CH>0.5%.

<p>Reproducibility: Comparison of mutant abundance at each polymorphic site for a single amplicon replicated on three platforms, located in two laboratories when considering all CH>0.5%.</p

PCR and UDPS errors.

<p>Experiment with clones. Point mutations and haplotypes found when cutting consensus point mutations (analysis by columns) or consensus haplotypes (analysis by rows) at 0.25% abundance (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083361#pone-0083361-t001" target="_blank"><b>Table 1a</b></a>) at a cut-off of 0.50% abundance (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083361#pone-0083361-t001" target="_blank"><b>Table 1b</b></a>). Err indicates the number of false segregating sites, and OK the number of true segregating sites.</p

Reproducibility: Quasispecies complexity measures for a single amplicon replicated on three platforms, located in two laboratories.

<p>Hpl stand for number of haplotypes, Eta for number of mutations, S for number of polymorphic sites, Mf for mutation frequency, Sn for normalized Shannon entropy and Pi for nucleotide diversity.</p

Number of reads per sample and strand at each data treatment step, and haplotype distribution at a consensus haplotype abundance >0.5%.

<p>Number of reads per sample and strand at each data treatment step, and haplotype distribution at a consensus haplotype abundance >0.5%.</p

Reproducibility: Measures of quasispecies complexity for ten amplicons replicated on GS-FLX and GS-FLX+ located in two different laboratories.

<p>Data from CH>0.5%.</p><p>Hpl haplotypes, Eta number of mutations, S number of polymorphic sites, Mf mutation frequency, Sn normalized Shannon entropy, Pi nucleotide diversity.</p