Proximal Chromosome 5 compared to the Ensembl v3 sequence assembly. (A) Shows the portion of the Chr 5 map detailed in the rest of the figure. (B) Shows TJL BSB/BSS backcross recombination map, with crosshatches for each crossover and heavier crosshatches for each position that contains a framework marker. (C) The T31 RH framework map for this proximal region. A 50-cR scale bar is included to the left of the chromosome line. Note that there are four markers that cosegregate at the top of the recombination map and another four that map two crossovers distally. D5Mit71, shown in plain text with a dashed line joining the maps, could only be mapped in the BSS cross, and its BSB position is estimated from data based on reading copy number of C57BL/6J alleles. The backcross mapping places this marker clearly proximal to D5Mit226 andD5Mit194. (D) The retention frequency graph for this part of Chr 5 shows the unusually high retention of theD5Mit71 marker that causes it to link poorly to the surrounding data. (E) The Ensembl v3 sequence assembly for this region. The sequence is shown to Mb scale (a 5-Mb scale bar is included to the right of the figure), with crosshatches for each MIT SSLP marker annotated in the sequence. Right-pointing arrows indicate gaps in the contig. The vertical double-headed arrow shows the region that is in inverted order relative to the recombination/RH map.