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The map also aids in assembly of reference genomes, gap-filling, and independent assessment of assembly accuracy.
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Is guidance by the human reference sequence in assembly of Neanderthal and Denisova genomes a potential factor in their reproduction of the reported human frameshift?
Reference mapping did not result in assembly of the full genome.
This error could happen in the construction of the clone, the mapping of the read to the reference genome, or in the assembly of the reference genome itself.
We were only able to confirm up to 616 nucleotides upstream of the putative transcription start site for the GSL2 gene due to a gap in the assembly of the reference potato genome in the upstream region of the GSL2 promoter.
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.
Another potential bias originates in the assembly of the reference human genome, which is more likely to use a longer allele within a heterozygous locus.
This high-density map should also be valuable when anchoring and orienting scaffolds in the assembly of the reference genome (Tuskan et al. 2006; Sato et al. 2012).
Accordingly, the high quality physical map of 5DS presented in this study, will not only contribute to the identification of genes through map-based cloning and but also aid in the assembly of the reference sequence of this chromosome.
Accordingly, the high quality physical map of 5DS presented in this study, with a density of 10.5 markers/Mb, will not only contribute to the identification of genes through map-based cloning and but also aid in the assembly of the reference sequence of this chromosome.
Computational analysis using raw sequences absent in the main assembly of the reference strain of D. melanogaster y ; cn bw sp supported the existence of additional haplotypes that must belong to other copies of the gene Sdic (Fig. 1B).
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