How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?

Table 10 Percentage of aligned reads and the false alignment rate for 218 CpG island simulation data

A. Mismatches with high quality (30-40)
Mismatch	Settings		SOAP2	Bowtie	BWA	Novoalign
1	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	13.80	13.84	13.80	17.25
	Suppress reads w/multiple alignments	aligned (%)	84.26	84.26	84.26	84.34
	Suppress reads w/multiple alignments	False alignments (%)	0	0	0.01	4.09
2	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	13.90	13.98	13.91	20.77
	Suppress reads w/multiple alignments	aligned (%)	84.39	84.22	84.39	84.23
		False alignments (%)	0.21	0	0.02	8.20
B. Mismatches with low quality (5-15)
Mismatch	Settings		SOAP2	Bowtie	BWA	Novoalign
1	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	13.79	13.83	13.80	15.93
	Suppress reads w/multiple alignments	aligned (%)	84.26	84.26	84.26	84.34
	Suppress reads w/multiple alignments	False alignments (%)	0	0	0.001	2.42
2	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	13.82	13.86	13.91	17.79
	Suppress reads w/multiple alignments	aligned (%)	84.39	84.22	84.39	84.23
		False alignments (%)	0.21	0	0.02	4.86

ISSN: 1756-0381