Uncovering the genetic diversity of Giardia intestinalis in isolates from outbreaks in New Zealand

Table 2 Sample Giardia assemblages according to results of Sanger sequencing compared with most abundant assemblages according to NGS

Sample no.	ID	Sanger	NGS	NGS reads
1	1997	BIV	BIV	55,235 reads in 15,404 unique sequences
2	1998	BIV	BIV	113,042 reads in 21,061 unique sequences
3	1999	BIV	BIV	136,387 reads in 25,493 unique sequences
4	10,015	AII	AII	118,718 reads in 23,734 unique sequences
5	10,046	BIV	BIV	141,257 reads in 24,507 unique sequences
6	10,047	BIV	BIV	95,812 reads in 19,814 unique sequences
7	10,048	BIV	BIV	95,836 reads in 28,269 unique sequences
8	10,049	BIV	BIV	106,343 reads in 24,744 unique sequences
9	10,936	BIV	BIV	8184 reads in 3121 unique sequences
10	10,937	BIV	BIV	144,483 reads in 39,869 unique sequences
11	10,938	AII	AII	116,354 reads in 33,518 unique sequences
12	10,939	BIV	BIV	121,820 reads in 21,446 unique sequences
13	10,940	BIII	BIII	20,678 reads in 6331 unique sequences
14	11,359	Unspecified	AIII	112,267 reads in 19,785 unique sequences
15	13,273	BIV	BIV	103,784 reads in 22,832 unique sequences
16	14,201	Unspecified	E	75,624 reads in 15,918 unique sequences

“Unspecified” denotes samples for which the assemblage could not be determined. The number of reads generated by NGS from each sample after filtering, trimming and dereplication are shown for reference
NGS next-generation sequencing

ISSN: 2049-9957