Only SNPs that were in agreement with the following parameters were used in the analysis: minimal coverage of 8, minimal variant coverage of 8, minimum variant frequency of 90%, and a p value ≤0.01.
This synthetic case-control data set was then analyzed with Annotate-it using the following filter settings: minimum 10× coverage, minimum variant allele frequency of 20%, only 'novel' variants, variants not found in the 1000 Genomes Pilot project, and variants not occurring in the control samples.
The working dataset of high coverage contigs was screened for SNPs using the CLC Genomics Workbench v. 5.5 (minimum coverage 8×, minimum variant frequency 10%, minimum number of reads per allele = 2, minimum central quality 20).
The working data set of high coverage contigs was screened for SNPs using the CLC Genomics Workbench v. 5.5 (minimum coverage 8×, minimum variant frequency 10%, minimum reads per allele = 2, minimum central quality 20).
Within the high coverage data set, 8,339 contigs contained SNPs that fell within our detection parameters (minimum coverage 8×, minimum variant frequency 10%, minimum reads per allele = 2, minimum central quality 20).
Parameters for SNP analysis using CLC Genomics Workbench: max # of gaps and mismatches 2, minimum average of quality of surrounding bases 15, minimum quality of central base 20, minimum coverage 1, minimum variant frequence 35%.
Single-nucleotide polymorphism (SNP) candidates were screened using the CLC Genomics Workbench 5.1 with the following parameters: window length, 11; maximum gap and mismatch count, 3; minimum coverage, 1; minimum variant frequency, 75%.
SNP calling parameters were set to minimum coverage = 5, and minimum variant frequency = 0.2.
Parameters were as follows: neighborhood radius = 5, maximum gap and mismatch count = 2, minimum neighborhood quality = 15, minimum central quality = 20, minimum coverage = 10, and minimum variant frequency = 35.0.
