Comparison of heterogeneous positions identified in TPA SS14 strain by Matějková et al. [14] and by the automated pipeline used in this study.

Abstract

<p>^aadditional intrastrain heterogeneous genome positions identified by Matějková et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] including 135141, 135144, 135149, 135220, 135227, 671982, 672004, 672016, 672025, 672026, 672027, 672028, 672036, 672039, 672040, 672041, 672042, 672043, 672044, 672154, 673088, 673119, 673511, 673545, 673550, and 673554 (according to the CP000805.1) were located in paralogous regions and therefore were excluded from the automated pipeline (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.s002" target="_blank">S2 Table</a>)</p><p>^bnumbers in parentheses show numbers of sequenced clones [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] or nucleotide frequency within individual Illumina sequence reads (this study); NA—not available</p><p>^cnot present in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.t002" target="_blank">Table 2</a>; heterogeneous positions were detected in raw Illumina sequencing reads but were excluded due to study criteria</p><p>^d these heterogeneous sites were not found among Illumina reads, but were identified among 454 reads (SRX000109)</p><p>^esee also <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.t003" target="_blank">Table 3</a>; independent DNA preparations showed clear differences in proportions of alternative alleles, ranging from 0.1 to 0.7</p><p>Comparison of heterogeneous positions identified in TPA SS14 strain by Matějková et al. [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004110#pntd.0004110.ref014" target="_blank">14</a>] and by the automated pipeline used in this study.</p