Table 1. Sequencing and mapping statistics.

DNA	Insert size (bp)	Read length (bp)	Reads	Aligned reads	Aligned (%)	Genome coverage (%)
PGM	∼500	108	130,266,728	110,189,736	84.6	99
Lambda-phage	∼200	101	83,149,385	25,949,607	31	44

Paired-end Illumina sequencing was carried out as described in Materials and Methods, and reads were mapped to the P. tetraurelia MAC reference genome using the BWA short-read aligner. The genome coverage is the fraction of the genome covered by at least 1 read. The depth of coverage with the PGM DNA is on average 165×. The depth of coverage with the lambda-phage DNA is on average 75× for the part of the genome that is covered. The PGM reads that were not aligned contain Paramecium mitochondrial and rDNA sequences, contaminating bacterial sequences as well as sequences present only in the MIC genome. In addition, a large proportion of the unaligned lambda-phage reads are from bacterial contaminants with AT-rich genomes; this DNA was not eliminated by the cesium chloride density gradient separation step of the phage library construction [28].