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Table 2 Results of the in silico SNP detection

From: Construction of 12 EST libraries and characterization of a 12,226 EST dataset for chicory (Cichorium intybus) root, leaves and nodules in the context of carbohydrate metabolism investigation

  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)
  1. 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.