Fig. 1

Whole-genome assembly contigs aligned against the 3D7 Reference. Contigs from Sample 303_1 (blue) aligned to chromosome 12 of 3D7 (black); var exon 1 sequences extracted from 303_1 (see “Methods”) and previously identified var exon 1 sequences from 3D7 are labeled as red dots on the contigs and chromosome. Exon 1 sequences extracted from the whole-genome assembly of 303_1 are found in chromosome regions similar to where 3D7 exon 1 sequences have been found. While some are found towards the center of the chromosome, a portion are also found on the ends, where complicated repeat regions and multi-gene families cause assembly issues and assembly contigs are seen to pile up in this area. Similar layouts for all 14 chromosomes for each of the 12 Malian clinical samples can be found in the Additional files