Table 2 consists of known VNTR markers used previously for MLVA analysis [6], [7] in addition to five newly identified tandem repeat differences (VNTR 1 5) discovered between NE061598 and Schu S4.
The closest matching haplotypes found were between a Maldivian individual from Addoo (Mal_045; Supporting Information Table S6) and the single Y-R1a1 SRY10831) Y-R1a1 SRY10831 Madagascar (Antanosy MAD20) that dindividualwo repeat difromences (one repeat each in DYS390 and DYS391).
Considering only the type of repeated unit, differences were also observed.
Scheffe's post-hoc test [ 23] however, found that only three percent of the observations for repeated test differences between any angle were significant.
All other haplotypes differed in at least four repeat differences.
Hybrid sequence assemblies were performed and a total of 56 validated SNP/INDELs and 5 repeat differences were identified in the D27 strain relative to published KIM 10+ sequence.
Since KIM D27 is a laboratory derived isolate of KIM 10+, the 56 SNP/INDELs and 5 repeat differences seemed suspiciously high, and it was possible that the reference KIM 10+ sequence had some errors.
Isolates were considered genetically related when the summed tandem repeat differences were <10 (3, 4, 6 ).
Only a limited number of single nucleotide polymorphisms and repeat differences could be investigated by this labour-intensive approach.
There were 966758 sites that only had one variant read for repeat differences and 1675976 sites that only had one variant read for SNP differences.
