Table 1 Amplicon Amplicon representation, successful base calling and average read count.

From: High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology

PCR product

CODON

Amplicon representation

Successful base-calling

average read count

count

percentage

count

percentage

Pfcrt.2

72

324

100

320

98,8

1129

Pfcrt.2

73

324

100

320

98,8

1129

Pfcrt.2

74

324

100

320

98,8

1128

Pfcrt.2

75

324

100

320

98,8

1128

Pfcrt.2

76

322

99,4

320

98,8

1128

Pfdhfr.1

16

324

100

323

99,7

2463

Pfdhfr.1

51

324

100

323

99,7

2335

Pfdhfr.1

59

324

100

323

99,7

2324

Pfdhfr.1

108

324

100

322

99,4

2448

Pfdhfr.1

164

324

100

323

99,7

2385

Pfdhps.3

431

324

100

322

99,4

774

Pfdhps.3

436

324

100

322

99,4

767

Pfdhps.3

437

324

100

322

99,4

767

Pfdhps.4

540

313

96,6

291

89,8

250

Pfdhps.4

581

320

98,8

311

96,0

1575

Pfdhps.4

613

320

98,8

311

96,0

1601

Pfmdr1.1

86

324

100

324

100

4734

Pfmdr.7

1034

318

98,1

307

94,8

440

Pfmdr.7

1042

318

98,1

307

94,8

440

Pfmdr.8

1246

324

100

322

99,4

1467

PfK13.1

84

324

100

324

100

2008

PfK13.2

224

322

99,4

320

98,8

755

PfK13.3

329

324

100

324

100

1511

PfK13.4

469

323

99,7

323

99,7

5963

PfK13.5

635

324

100

324

100

5816

Mito.1

base 772

324

100

324

100

2496

Mito.2

base 1283

324

100

324

100

3224

Mito.3

base 2383

324

100

324

100

5015

  1. The table shows how many of the samples were found with pertaining reads corresponding to the various amplicons, after quality trimming (as sample count and percentage), as well as for how many samples successful base-calling was performed (requires a minimum z-score of 1.96). For pfK13 and for the mitochondrion, a position for each amplicon was analysed. Some of the SNP positions are located in the same amplicon. The table also lists the name of the individual amplicons, and Fig. 3 can be referred to for illustrations of the length and position of the amplicons within the various genes.
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