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Table 1 Whole-genome sequencing statistics

From: Identification of pathogen genomic variants through an integrated pipeline

Experiment ID

Data source

Background strain

# of genomes

Resistance

Gene conferring resistance

Dd2 (parent)

[6, 10–12]

n/a

1

Chloroquine, Mefloquine, Pyrimethamine

n/a

3D7 (parent)

[12]

n/a

1

Sulfadoxine

n/a

KAD707 and 458

[12]

Dd2

4

Imidazolopiperazine

pfcarl

CladoR

[10], this study

Dd2

3

Cladosporin

pfkrs1

NITD609 (KAE609)

[6, 11]

Dd2

3

Spiroindolone

pfatp4

NITD678

[6, 11]

Dd2

3

Spiroindolone

pfatp4

Evo

[6]

3D7

14

Atovaquone

mal_mito_3

  1. Whole genome sequencing data acquisition statistics from each of the experiments used to validate the pipeline. Note that all of the lines with variants to be called were sub-cloned before sequencing and were sequenced as 70 bp paired end reads, except the KAD (imidazolopiperazines resistant) lines, which were sequenced as 60 bp single end reads. Library preparation details for sequences obtained from previous studies are available in their respective manuscripts. Library preparations for sequences obtained for this study (those resistant to cladosporin), are as follows: 200 bp fragments with 70 bp reads were prepared according to the manufacturers instructions using the Illumina NexTera XT sample preparation kit with accompanying primers and sheared using a Covaris E220x machine.
  2. n/a – not applicable.