Comparison of Next-Generation Sequencing Systems

Table 2

Comparison in alignment between Ion Torrent and HiSeq 2000.

	Ion Torrent^a	HiSeq 2000^b
Total reads num	165518	205683
Total bases num	18574086	18511470
Max read length	201	90
Min read length	15	90
Map reads num	157258	157511
Map rate	95%	76.57%
Covered rate	96.50%	93.11%
Total map length	15800258	14176420
Total mismatch base	53475	142425
Total insertion base	109550	1397
Total insertion num	95740	1332
Total deletion base	152495	431
Total deletion num	139264	238
Ave mismatch rate	0.338%	1.004%
Ave insertion rate	0.693%	0.009%
Ave deletion rate	0.965%	0.003%

^a: use TMAP to align; ^b: use SOAP2 to align.