The telomeric sequence (TTTAGGG) n, first identified in A. thaliana (Richards and Ausubel 1988), has the most loci (23,926) of any tandem repeat motif and the most overall sequence coverage (at ∼2.1 Mbp, or ∼0.01% of the genome).
We routinely pick a total of 192 clones (or two 96 well blocks) per viral sample for bidirectional sequencing as this represents the most affordable sequence coverage to efficiency ratio.
The reason for the observation of several phylogenetic lineages assigned to one single individual is most likely the low sequence coverage since it can lead to more false positive SNP calls.
The assembly had more than 3000 high quality sequence reads and 10 fold sequence coverage in most regions.
Surprisingly, the highest yield of sequence-informative fragment ions from protein backbone cleavage was obtained for the most basic protein, Melittin, whereas sequence coverage was smallest for the acidic proteins, Ferredoxin and BASP1 Δ121 216).
Rarefaction analysis showed clear asymptotes for both communities, suggesting that there was sufficient sequence coverage to detect most expressed genes.
In the context of the GC-rich genome of B. pertussis, most platforms gave similar uniformity of sequence coverage, with the Ion Torrent data giving slightly more uneven coverage.
For most of the samples at least 10x sequence coverage was achieved for more than 90% of the target bases.
Among the teleost genomes with high sequence coverage, zebrafish is the most closely related species to catfish [ 46].
While distinct in their approaches, they are most comparable in design (making use of sequence coverage and soft clipping).
