| Color | Genetic, YAC, RH | BAC End Pairs | Clone Overlaps |
|---|
| White | No markers placed | All clone bridges in same contig | Best overlap with succeeding clone or no overlaps |
| Blue | Marker consistent with alignment of STS map | Clone bridges two adjacent contigs | |
| Green | Marker slightly inconsistent with alignment of STS map | Clone bridges close contigs | Overlap with non-adjacent clone in same contig |
| Pink | Marker inconsistent with STS map, same chromosome | Mulitple clones bridge to distant contig, same chromosome | Overlap with clone on different contig, same chromosome |
| Red | Marker inconsistent with STS map, different chromosome | Mulitple clones bridge to contig on different chromosome | Overlap with clone on different chromosome |
| Yellow | Marker not placed on any accession in contig, but alignment with STS map indicates it is in contig | | Overlap with clone not used in assembly |
