On Donnerstag 03 Dezember 2009 Shai Uliel wrote: > Can you give the explanation when MIRA write SNP (W,R....) and when > MIRA create two contigs ?????? Did your keyboard got stuck on the question mark? :-) The simple explanation: if MIRA feels certian enough, it'll creates two contigs. If not, it looks whether there's enough evidence to call a single base as consensus (ACGT). If two or more bases have approximately the same probability to be a real base, it calls a IUPAC code base (W,R,...). Regards, Bastien -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html