In order to optimize and speed-up the analysis, tally (Davis et al., 2013) is being used for de-duplicating the sequence fragments.
Typically, unlike other known transposable elements, Helitrons do not contain repeats of their terminal ends and do not duplicate the host sequence upon insertion (Kapitonov and Jurka 2001).
Using the same primers, we failed to duplicate the same sequencing results in JPB34342 and JPB34343 as discovered by Robertson et al. [ 19].
The identification of an 80 kb transposition that is present on the same chromosome, but distant enough to allow for intermittent CO events, generated haploid genotypes that either lost or duplicated the transposed sequence.
Inspection of a sample of these contigs suggests that they could represent small insertions/deletions within the aligned sequence, duplicated sequence, poorly assembled sequence, or segments in the CB4856 with remaining problems.
After sequence alignment and removing potential PCR duplicates, the sequencing depth varied from 8.2× (CS) to 12.4× (WR), which was sufficient for CNV detection, and the average coverage with respect to the chicken reference genome sequence was 97.2% (Table 1).
We correlated divergence of WGD duplicates at the sequence and network level.
SAMtools v0.1.7 [ 31] was used to remove potential PCR duplicates among the sequence reads and to call SNPs.
To remove the PCR duplicates of the sequence reads, which can be generated during the library construction process, the rmdup command of SAMtools [ 39] was used.
It was found that the entire ~3810 bp sequence representing the segmental duplication maps to a single cDNA (accession # AY119274) suggesting that the duplicated sequence containing the four genes is expressed as a common primary transcript.
