An expanded global inventory of allelic variation in the most extremely polymorphic region of Plasmodium falciparum merozoite surface protein 1 provided by short read sequence data

Table 2 Major allelic types of msp1 block 2 among the assembled short read sequences

Region	Number	Number (and %) of each allelic sequence type assembled
Region	Number	K1-like	MAD20-like	RO33-like	MR recombinant
Africa	787	367 (46.6)	185 (23.5)	204 (25.9)	31 (3.9)
Asia	735	172 (23.4)	436 (59.3)	126 (17.1)	1 (0.1)
All	1522	539 (35.4)	621 (40.8)	330 (21.7)	32 (2.1)

For short read sequences from each of the infection isolates in the Pf3k project, assembly was performed on paired end short read sequences for which one paired read mapped to a reference msp1 gene sequence, and also on sequences that mapped to a library of reference msp1 block 2 sequences. This yielded a total of 1522 complete msp1 block 2 sequences from among the 2400 isolates with raw data, as some isolates did not have sufficient read depth to allow assembly of full msp1 block 2 sequences. The number of sequences identified as belonging to each major allelic type is shown, showing similar proportions to those identified on the basis of alignment to the library of allelic reference sequences (Table 1)

ISSN: 1475-2875