A eukaryotic genome assembly may be entirely clone-based, entirely a product of the Whole Genome Shotgun sequencing (WGS) or a combination of two or more methods. For example, the current human reference assembly (GRCh38) is largely clone-based, but it does contain limited amounts of WGS. In contrast, the current chicken assembly (GRCg6a) is mostly derived from WGS, but have some chromosomes comprised predominantly from clones.
For many organisms with assembled genomes, NCBI may also have information for corresponding genomic clone libraries. Regardless of the assembly methodology, NCBI staff attempt to place (map) genomic clones from the registered libraries on the assembly. This is done by aligning either full insert or clone end sequences to the assembly to define the most likely genomic position for the clone. Clone placement enables users to find individual genomic clones that contain sequence content of interest. In some cases, individual clones can be ordered from genomic library producers, and serve as laboratory reagents for further analyses.
Clone placements have various attributes, such as concordance. Concordance refers to the size of the clone placement relative to the assembly, as well as the end sequence orientations. You can also use concordance/discordance of the placed clones to evaluate assembly quality identify genomic regions containing possible structural variation (learn more by watching this tutorial on Using Clone Placements to Interpret Genome Assemblies).
For details on how NCBI generates clone placements, definitions concerning clone placements, and interpretation of clone placement tracks, please refer to the Clone FAQs document at the Clone FTP site.