Table 2.

Results of the in silico SNP detection

	MM	MM.good	Manual selection
Number of contigs (CAP3)	1,546	1,546	653
SNP selection criterion (occurrence)	all SNPs	at least 2 times	more than 2 times
Number of SNPs containing contigs	1,417	255	64
Total number of SNP detected	43,656	1,886	294
Average SNP frequency in contigs	30.8 (1/25 bp)	7.4 (1/105 bp)	4.6 (1/198 bp)

The SNP/indel discovery pipeline generates contigs. Depending on the selection stringency (MM, MM.good and Manual selection), the number of contigs included in the analyses ranged from 1,546 down to 653 when the selection was restricted to clusters containing a least three sequences (manual). Within these contigs, those effectively containing SNPs are reported as well as the total number of SNPs detected and the average SNP frequency in the contigs.