Under the criteria of minimum coverage (read depth) of four and the minimum variant frequency of two, the variations compared to the reference sequence were counted as SNPs.
For identification of SNPs inherited from one heterozygous parent and one homozygous parent, the minimum variant frequency was set to 20% to allow variation from the expected haplotype frequency of 25/75%.
To classify whether mismatches were sequencing errors or genomic variations, parameters were set as follows: minimum depth, 30; minimum variant frequency, 35%; least mismatch count, 20; and homo/heterozygote fold change, 2. RAP-DB was utilized to locate the discovered SNPs.
SNP calling parameters were set to minimum coverage = 5, and minimum variant frequency = 0.2.
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).
The average value has minimum variation compare with exact value.
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.
The minimum fundamental frequency (F0min) has the highest degree of inter-individual variation, among the acoustic parameters used to describe the phonic structure of fallow deer groans [41].
This requires a minimum light frequency, in agreement with experiment.
fmin minimum permissible frequency.
where b mw is minimum frequency bin and b mi is minimum interval frequency bin.
