Under this proposal, the experts would define the minimum coverage "within statutory parameters" set by Congress.
Deletion/insertion polymorphism (DIP) candidates were screened by using the CLC Genomics Workbench 5.1 with the following parameters: minimum coverage, 1; minimum frequency, 50%.
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).
We used the SNP detection function in CLC Genomics Workbench, based on the neighborhood quality standard (NQS) algorithm, using the following parameters: minimum coverage = 5; minimum central base quality = 30; average base quality over a window length of 11 nucleotides = 15; and, minimum allele frequency = 35%.
We used the deletion and insertion polymorphism (DIP) function in CLC Genomics Workbench using the following parameters: minimum coverage = 5; minimum allele frequency = 35%; and, maximum expected variations = 2. INDELs were filtered in a similar manner as SNPs, with those near other variants and within the PAR being removed.
Initial parameter values were: minimum coverage depth 3, minimum SNP quality 20, minimum indel quality 50, with other parameters such as window size and nearby SNP and gap density left at their defaults.
12 The global identification of potential A to I (G) editing sites was called using VarScan, 13 with the following parameters: a minimum coverage depth of 10, a variation frequency of more than 10% and a base quality of more than 15 (figure 1A).
All other parameters, such as minimum coverage, minimum alternative allele frequency, and strand bias were the same between the two settings (parameter files provided).
In addition, the SNP detection parameters required a minimum coverage of eight reads at a polymorphic site to be included in the data.
