Table 2: Comparison in alignment between Ion Torrent and HiSeq 2000.

Ion TorrentaHiSeq 2000b

Total reads num165518205683
Total bases num1857408618511470
Max read length20190
Min read length1590
Map reads num157258157511
Map rate95%76.57%
Covered rate96.50%93.11%
Total map length1580025814176420
Total mismatch base53475142425
Total insertion base1095501397
Total insertion num957401332
Total deletion base152495431
Total deletion num139264238
Ave mismatch rate0.338%1.004%
Ave insertion rate0.693%0.009%
Ave deletion rate0.965%0.003%

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