This strategy can be used to physically map duplicate loci, provide order information for loci in a small genetic interval or with no genetic recombination, and loci with conflicting hybridization-based information.
Our data indicate that in addition to anchoring the genetic and physical maps, the pools can be used to define local marker order, resolve conflicting hybridization-based marker: BAC assignments, and rapidly map duplicate factors or members of a gene family.
For example, the CART method (classification tree-based models) could be used for mapping duplicates and defining clusters of records, which have to be seen not as duplicates but "n-plicates".
However, several other studies have already evaluated variant detection sensitivity with exome data and identified numerous factors that influence variant detection sensitivity including coverage, quality of alignment and mapping, duplicates, strand bias, and type of algorithm used [ 5, 27- 29].
For copy number analysis, we completed read mapping, duplicate removal, and re-alignment as described above.
Third, we will examine divergence of homologous arms by mapping duplicated loci.
These challenges include (1) mapping duplicated reads to a single reference genome, (2) the difference in similarity between the subgenomes of an allopolyploid and the diploid reference sequence, (3) gene conversion, (4) allopolyploid autapomorphies, and (5) diploid autapomorphies.
Reads of the analysis target should be preprocessed by read-mapping, duplicate marking (if applicable), and indel realignment; this entity is depicted as a stack of BAM-format files in Figure 1.
Data mining of the FAERS requires complex data processing to obtain the final dataset; in particular, an ad hoc drug mapping, duplicate detection and removal as well as management of missing data.
In this new map, 693 duplicated loci were identified by 326 SSR primer pairs, with 574 duplicated, 111 triplicated, and eight tetraplicated loci (Additional file 2: Table S2).
Note that the Digital Sanborn Maps largely duplicates the CRL microfilm collection.
