Physical and Optical Maps

Optical, Physical and Genetic Maps
Genetic Map

Jim Kronstad at the Vancouver Genome Sequence Centre compiled a genetic map consisting of finger print contigs (FPCs) made up from overlapping BAC clones. The paired end sequences of these BAC clones have been incorporated into our assembly and thus we can compare the order of clones between the two maps for independent validation.

Using a set of 2013 unambiguously placed BAC clones, we associated the 18 largest supercontigs (representing >98% of the genome) with 19 finger print contigs. The comparison shows that the two independent data sets strongly support each other with over 92% correspondence of order between BACs in the assembly and the FPCs*.

Please note! The order of supercontigs and fingerprint contigs in the image to the right is arbitrary! We do not know the relative locations of supercontigs or chromosome information.

SupercontigFinger Print Contig (FPC)# BACs in FPC% BACs with same order in FPC*#BACs on different FPC
11,19162,12098%,96%0
2518895%3
3315184%0
41218997%0
51717288%0
619,753,12786%,96%0
7813496%0
82011586%0
9138686%0
1018,47,7685%,96%0
1111,1466,1281%,91%0
12109097%0
1397397%0
1426680%0
15107397%0
16162190%0
17151794%0
18171190%0

The details of this correspondence can be downloaded from assembly2fpc_map.txt

Legend

  • Supercontigs on the left (with the individual contigs displayed in alternating black and green segments)
  • Fingerprint contigs on the right
  • Lines indicating the center of a BAC clone on the supercontig and on the FPC

* "Correspondence of order" between BACs in the assembly and FPC contigs allows for minor local rearrangement on the FPC map (within 10 FPC map units). We observe 59% overall correspondence using strict ordering.