Identification of pathogen genomic variants through an integrated pipeline

BMC Bioinformatics

Table 4 CNVs detected using WGS and genomic microarrays

Strain	Position (Micr.)	Position (Seq.)	Presumed relevant gene	Copy number (Seq.)	Orientation (Seq.)
all 3D7 derived lines	chr12_974243-975980	chr12_974276-976007	pfgch	2	tandem
all Dd2 derived lines	chr5_892863-968421	chr5_892872-968429	pfmdr1	2	tandem
all Dd2 derived lines	chr12_970985-975864	chr12_971011-975866	pfgch	2	tandem
Evo5a/b	chr1_428540-643352	chr1_428538-643350	pfmrp1	2	unknown*
CladoR_clone1	chr13_1996541-2018534	chr13_1996635-2018727	pfkrs1	3	tandem
CladoR_clone2	chr13_1996668-2055132	chr13_1996621-2055107	pfkrs1	3	tandem
CladoR_clone3	chr13_2001466-2051201	chr13_2001482-2051233	pfkrs1	3	tandem
NITD678_clone1	chr12_510069-633784	chr12_510123-633834	pfatp4	2-3	tandem

*Orientation could not be determined as the amplification continued into the telomeric region.
Predicted CNV calls with position from both WGS (Seq.) using Platypus and microarray data (Micr.), with predicted copy number compared to the 3D7 reference and orientation of the amplification as determined by Platypus.

ISSN: 1471-2105