High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum

BMC Genomics

Table 5 Five known copy number differences detected between parental strains using WGS read depth.

Chromosome	Type	No. of 2.5 kb windows	Significant windows (p < 0.001)	Highest Chi-square value
2	Deletion - in both	15	0	3.99
5	Amplification - 7C126	33	33	1212
9	Deletion - in both	52	13	50.6
12	Amplification - 7C126	1	1	85.44
12	Amplification - SC05	64	63	356.03

Read alignment density was consistent with the known CNV alleles except for chromosome 9, where smaller insertions and deletions are detected within a larger shared allele.

ISSN: 1471-2164