Table 2.

Different properties presented in mate-pair and paired-end strategies.

Different properties	WGS-MP	WGS-PE
Recommended sequencing depth	About 5× genome size	Not less than 10× genome size
Flanking sequence information	Many and valuable	Little
Insertion sites and flanking sequence validation	Easy	Very easy
Number of false positives	Few	Extremely high
True positives in total results	High	Intermediate
Evaluation of copy number	Easy	Easy
Plasmid backbone residue analysis	Easy	Easy