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Table 5 Sequencing metrics for clinical isolates from The Philippines

From: Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

ID

Serotype

Genotype

Reads passing QC

Coding-Region Coverage (%)

Nucleotide Consensus Similarity (%)

Single-plex Amplification Result (5′ → 3′)

1X

20X

1X

20X

1

2

3

4

5

130,158

1

IV

6852

99.80

79.22

99.57

99.86

+

+

+

+

130,104

2

Cosmo.

12,932

99.99

94.57

99.80

99.92

+

+

+

+

1,601,002

3

I

4605

99.93

89.40

99.17

99.70

+

+

+

+

+

130,343

4

II

7805

99.90

90.40

99.24a

99.70a

+

+

+

+

  1. aSeveral of the single-plex reactions were unsuccessful (−), and had to be repeated using primers from the multiplex primer set to generate the reference amplicons that were sequenced on the Illumina platform. The single-plex approach was unable to generate an amplicon covering the 3′ end of the DENV-4 genome, despite repeated attempts with a range of primers. Therefore, it should be noted that the accuracy of the multiplex-generated consensus sequence is not for the full coding region, but only accounts for 10,117 of the 10,163 coding bases