FIGURE 2. Example contig from the whole-genome BAC map.

Portion of contig shown is localized to chromosomal region 8q21, composed of 836 BAC clones ordered by restriction fingerprint mapping. a, Contig summary information. Only 287 of the 836 clones are displayed. Redundant clones are 'buried' in their parent clones as indicated by the + and * clone name suffices (see (c)). The contig contains 193 markers; 77 clones have been selected for sequencing. Contig length: 1,552 unique restriction fragments (6Mb). b, Markers associated with clones in the display. Green: specifically associated with clone N0363E06 (aqua in c). There are 69,507 markers currently in the database associated with clones, largely by ePCR. Only one marker of the 62 shown is inconsistent with the 8q21 localization of this contig (D17S978, red underline). This is probably not a unique marker in the genome as the clone with which it is associated also contains several chromosome 8 markers. c, Partial display of the contig, showing 112 of the 287 clones visible with this view. Blue, example clones selected for sequencing. These clones were believed to overlap as they shared several restriction fragments; overlaps have been confirmed by working draft sequence. d, Data associated with the clones in c. FISH data (for example JMF-8q21.1) is consistent, except for one clone (N005M18, 9q22, red underline), probably owing to a clone-tracking error (the placement of the associated accessioned sequence (AC022821) in this location is supported by sequence overlap with surrounding clone sequences (clone N0813B08, AC069139)). Chromosomal localization of clones using STSs derived from BAC end sequences (for example, COX_8) is also consistent, with one exception (N0028G16, chromosome 14 COX_14, red underline), probably owing to incorrect association of an end sequence with a clone name in the BAC end sequence database. GenBank accession numbers are indicated. Sequences were mapped to the associated clone using in silico restriction digests, BAC end sequences and sequence overlap. Around 11.5% of the accessioned sequences have an incorrect clone name in their GenBank record, so proper placement of the sequence relative to the physical map was achieved in this manner. N00792N11 and N0096I13 are associated with accessioned sequences AC026617 and AF181449, respectively. The incorrect clone name referenced in their sequence records is indicated. e, Markers associated with the GeneMap'99 radiation hybrid map. Several are associated with clones in this contig (c), further positioning this contig within the genome.