Identification of Trichinella taxa by ITS-1 amplicon next-generation sequencing with an improved resolution for detecting underrepresented genotypes in mixed natural infections

Table 4 Differences in sequence variations of NGS reads mapped to the Trichinella chanchalensis reference for the L1 pools from wolverine and American marten

Host species	Variation type	Nucleotide position	Change	AO	Depth*
Marten	Indel	201—202	CA—> Deletion	184	1226
	SNP	160	A—> G	187	1226
	SNP	46	G—> C	187	1226
Wolverine	SNP	289	T—> A	21,741	120,382

^*Vastly different depths of coverage were achieved due to not only different numbers of quality-filtered merged reads mapped to the T. chanchalensis reference between the two host species but also different numbers of total reads generated with the use of MiSeq Reagent kits with 'standard' and 'nano' flow cell
AO, number of alternate observations; SNP, single nucleotide polymorphism

ISSN: 1756-3305