Variants were detected by Quality-based Variant Detection Tool using following parameters; neighborhood radius: 5, maximum gap and mismatch counts: 5, minimum neighborhood and central qualities: 30, minimum coverage: 10, minimum variant frequency: 10%, and maximum expected alleles: 4. Non-specific matches were ignored and bacterial genetic code was used.
This means that maximum gap and speed are not the only criteria but also convenience.
The following quality filtering criteria were enforced: neighborhood radius = 5, maximum gap and mismatch count = 2, minimum neighborhood quality = 15, and minimum central quality = 20.
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.
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%.
For SNP Detection in the CLC Bio Genomics Workbench, the parameters included a window length of 9, a maximum gap and mismatch count of 4, a minimum quality of the SNP base of 20, a minimum average quality of the nucleotides surrounding the SNP of 15, and a minimum read coverage for a SNP of 6.
Quality-based variant detection in CLC was then run on this mapping in order to identify variants between the two subspecies with the following settings: neighbourhood radius: 10, maximum gap and mismatch count: 5, minimum neighbourhood quality: 20, minimum central quality: 30, ignore non-specific matches, ignore broken pairs.
Post-operative fill parameters such as mean stem-to-canal ratios and mean minimum and maximum gaps between the stems to the cortical bone in different sections and areas were compared.
The maximum gaps are 18.4, 37.5, and 15.5 cM for Set 12, Set 52 and Sets 12 and 52 combined, respectively.
Illumina sequence-reads were assembled de novo with Geneious 7.0.528; the assembly parameters were: 1) minimum overlap 70 bp; 2) minimum overlap identity 90%; 3) maximum gaps per read 5%; and 4) maximum gap size 5 bp.
