Sequencing and microarray results summary.

n/a: not applicable, SNV: single nucleotide variant, Mb: Mega base, *SNVs in parenthesis were within 15 kb from a chromosome end and could not be confirmed by WGS. ctr: control parasite lines without

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Microarray probe summary.

Note: The median intensity and the presence call % of all probes on each array was measured using dChip software. The standard deviation (SD) was calculated from three experiments. The presence call %

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SMRT sequencing results summary.

§as estimated by gel electrophoresis of cloned expansion fragment excised from plasmid backbone. ¶As compared with Sanger sequencing. *Alignment based on reference genome sequence (NC_000022.11; GI: 5

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