Table 2. The percentage of read pairs that aligned to each reference.

The percentage is provided of read pairs from a subset of datasets that aligned to each reference for bwa-aln with default parameters and bwa-mem with seed lengths from 18 to 30 nt.

Dataset	Reference	aln	18	19	20	21	22	23	24	25	26	27	28	29	30
Plasmodium–human	Human	10.2	24.1	22.4	21.2	20.4	19.9	19.6	19.4	19.2	19.1	19.0	18.8	18.7	18.5
Plasmodium–human	Plasmodium	78.1	83.6	83.3	83.1	82.9	82.8	82.6	82.4	82.3	83.6	83.3	83.1	82.9	82.8
Plasmodium–human	Combined reference	88.3	97.1	96.9	96.7	96.5	96.3	96.1	95.9	95.7	95.5	95.3	95.1	94.9	94.6
Brugia–Wolbachia	Brugia	91.9	94.4	94.0	93.8	93.8	93.7	93.7	93.6	93.6	93.6	93.6	93.5	93.5	93.5
Brugia–Wolbachia	Wolbachia	2.7	3.3	3.0	2.9	2.9	2.9	2.9	2.9	2.9	2.9	2.8	2.8	2.8	2.8
Brugia–Wolbachia	Combined reference	94.5	96.4	96.2	96.1	96.1	96.1	96.1	96.0	96.0	96.0	96.0	96.0	96.0	96.0
1000 Genomes	Human	95.9	99.7	99.6	99.6	99.6	99.6	99.5	99.5	99.4	99.4	99.4	99.3	99.2	99.2