Table 9.

Percent of 100,000 paired human reads from NA12878 in 1000 genomes (SRR016607) of length 101 bp mapped concordantly to the human genome

NextGenMap	NextGenMap+	NextGenMap+
	MaxSSmap_fast	MaxSSmap
83.5 (0)	85.8 (0.7)	87.6 (1.2)
Time in minutes to map paired reads
1.5	1295.9	2242.4

Concordant reads are pairs that are mapped within 500 base pairs. Also shown in parenthesis are discordant reads (mapped positions at least 500 bp apart) and the time in minutes. In NextGenMap+MaxSSmap we re-align pairs with MaxSSmap where at least one read in the pair was unmapped by NextGenMap or the pair is discordant. Thus, NextGenMap shows zero discordant pairs because we re-align them with MaxSSmap.