Variation and annotation map of eight MHC haplotypes. The map represents the complete reference sequence (orange bar split into three 1.6 Mb sections) labelled PGF and marked with a scale (Mb) and approximate megabase positions on the NCBI36 build of chromosome 6 (grey milestones). Below the reference sequence are arrows representing gene positions and orientations colour-coded for variation status (invariable, black; with synonymous variation only, green; with non-synonymous, conservative variation, red; with non-synonymous, non-conservative variation, purple; see Table ) and their symbols on a band denoting MHC class (extended class I, green; class I, yellow; class III, pale orange; class II, light blue; extended class II, pink; outside MHC, pale grey). Above the reference sequence, coloured bands represent the sequences of the other seven haplotypes (COX, orange; QBL, mauve; APD, yellow; DBB, green; MANN, light blue; SSTO, dark blue; MCF, purple) with sequence gaps in dark grey; the RCCX hyper-variable region shown with green (C4A block) and/or red (C4B block) or black (block absent), and the HLA–DRB hyper-variable region in shades of blue-green. Above each haplotype bar, a bar-graph represents total variation between the haplotype and the reference sequence (total variations/10 kb) in dark red. Re-examination of the sequence AL645922 from the PGF haplotype, which contains the RCCX region, has shown that the original assembly was erroneous. Correction of these errors leads us now to the conclusion that the C4A gene precedes the C4B gene in this clone sequence. This new gene order is reflected in Fig. 2