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Table 2 Test of simulated data with overlapping amplicons

From: cFinder: definition and quantification of multiple haplotypes in a mixed sample

Test Clone variants Default Infer relationships
% Hits % Hits
A 1 23.8 5
  3 23.8 5
  1, 3* 14.3 3 28.6 2
  1, 2 4.8 1
  2 4.8 1
  2, 3 4.8 1
  1, 2, 3* 14.3 1
B 3* 43.8 21 37.5 6
  2* 37.5 18 31.3 5
  2, 3 8.3 4
  3, 4 8.3 4
  2, 4 8.3 4
  4 6.3 3
  1, 4 2.1 1
  1, 3 2.1 1
  1, 2 2.1 1
  2, 3, 4* 18.8 3
  1, 2, 3, 4* 6.3 1
  1. Comparison of using the infer relationship option to detect haplotypes that are scattered over multiple amplicons. The column clone variants holds a list of variants (numbered according to Fig. 3, design of the test cases) where “1, 3” means that the clone has variant 1 and variant 3. Default analysis yields just occurring haplotypes on simple amplicons while ticking the checkbox for inferring haplotypes manages to identify the connected variants. If clone was not detected it is marked with a dash (–), true haplotypes (used for simulation) are marked with a star (*)