This process uses a cut-off range of 90% to 15%, with higher cut-offs corresponding to more stringent peak detection, reflected in the FDR calculation.
This process uses a cut-off range of 90% to 15%, with higher cut-offs corresponding to more stringent peak detection, as reflected in the FDR.
Note that using a much more stringent threshold for ortholog detection, an E value of 10−, altered the final data set very little (3,920 clusters compared with 3,961).
For replay content assessments (below), we used a more stringent criterion for replay detection by performing the shuffles for each putative replay event on the one trajectory with the strongest replay score.
These sequences showed no matches to ESTs or known genes, and they exceed more stringent conservation criteria for detection of intergenic regulatory elements (>70% identity per 100 bp [ 21]).
The oak SNP frequency was still lower, probably due to more stringent criteria used for SNP detection.
These results were similar (duplications in 75% of the families surveyed), when more stringent cut-offs for homology detection were applied (see figures S1, S2 and S3 in the additional file 1).
Based on the findings in 96-plex validation and analysis of assay failure, we applied more stringent filtering in the SNP detection approach by increasing SNP score cutoff and removing genes with exon-intron boundaries and paralogous genes more than 90% similarity (Filter 3).
If paralogous genes affect the detection of polymorphic SNPs, more stringent filtering will not improve validation rate.
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