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

Table 9 Percentage of aligned reads and the false alignment rate for 3000 exon 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 (%)	0.76	0.77	0.76	4.83
	Suppress reads w/multiple alignments	aligned (%)	98.69	98.65	98.68	98.69
	Suppress reads w/multiple alignments	False alignments (%)	0	0	0	4.13
2	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	0.78	0.78	0.76	8.95
	Suppress reads w/multiple alignments	aligned (%)	98.69	98.68	98.68	98.67
		False alignments (%)	0	0	0	8.26
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 (%)	0.77	0.75	0.76	3.10
	Suppress reads w/multiple alignments	aligned (%)	98.69	98.65	98.68	98.69
	Suppress reads w/multiple alignments	False alignments (%)	0	0	0	4.13
2	Randomly report one alignment	aligned (%)	100	100	100	100
	Randomly report one alignment	False alignments (%)	0.77	0.81	0.76	5.49
	Suppress reads w/multiple alignments	aligned (%)	98.69	98.68	98.68	98.67
		False alignments (%)	0.02	0	0	4.78

ISSN: 1756-0381