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Whereas the Roche/454 platform has been used widely for the detection of low-frequent drug resistant variants, more recently developed short-read MPS technologies have the advantage of delivering a higher sequencing depth at a lower cost per sequenced base.
Thus, deferred cluster calling can be a valuable tool to efficiently achieve a higher sequencing depth for low-diversity sequencing libraries.
A higher sequencing coverage may result in detection of more GCNVs.
For mutations in the conserved region to be effectively detected, perhaps a higher sequencing depth/minimum read percentage with non-reference nucleotide coverage needs to be achieved.
However, de-novo sequencing differs from re-sequencing because it requires the generation of an informative and robust sequence with a higher sequencing depth.
Point #2: As mentioned in the expanded Materials and methods, we required a higher sequencing depth for the Nascent-Seq data than for the RNA-Seq for this exact reason, i.e., less exonic signal in Nascent-Seq data.
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Allowing for a higher sequence divergence improved the mapping (i.e.: fewer broken pairs).
Due to a higher sequence similarity, the GyrA from E. coli was picked automatically as a prototype [19].
Interestingly, E1b displayed a higher sequence conservation (94.4% between mouse and rat, 69% between mouse and human) than E1a (72.7% between mouse and rat, 59.8% between mouse and human).
A higher sequence identity was detected in the N-terminus (53%; 15/28), the ankyrin repeats (60%, 53/88), and the SAM domain (39% (26/66).
Thus, a higher sequence variability of Motif A among various proteins is consistent with the possible recognition of different substrates.
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