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Other types of variations were rarely observed.
Other types of variations were not analyzed as there are not highly reliable predictors for them.
In addition, other types of variations in CDS sequences were evidenced.
The option to search for other types of variations is thus also provided, which identifies significantly more matches.
Currently, the most well-known methods for detecting the tandem duplications (along with other types of variations) using just the paired-end NGS data include SVDetect [ 20], CNVer [ 21], SPANNER [ 22], inGAP-sv [ 23], BreakDancer [ 11], GASV [ 14] and CREST [ 16].
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It is important to acknowledge that different types of uncertainty have to be dealt with, such as uncertainty due to sample size and geographical, spatial or other types of variation.
In addition, validation rates for data from the 1000 genomes project averaged a validation rate of 1.8%, and similar to our study, large SVs were easier to validate than other types of variation.
Typically, as in this study, the genetic variants are SNPs, but other types of variation could be used.
Other types of variation, including within-block heterogeneity, however, are not readily discernible in the data, and are probably impossible to control.
Thus, CN seems to be more variable in larger populations, following the similar patterns as other types of variation such as SNPs [ 25] and microsatellites [ 23].
As we didn't obtain the full length cDNA of the gene in these lines, we concluded that there might be other types of variation that caused loss of gene function.
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