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A HANDY 2005 REFERENCE FOR DECIPHERING MAPS AND THE VARIOUS NEIGHBORS MAPS

Current Maps (as of 2005)
+ IBM2

+ IBM2 FPC0507

   Genetic coordinates for loci in anchored contigs
      FPC
         -anchored contigs
         -markers with 2 BAC hits in the contig
         -create locus name based on probe, typically an overgo
         -consensus band (CB) coordinates for each locus
      IBM2
         -genetic coordinates for IBM2 anchors
      Oher genetic maps
         -some FPC marked sites match a mapped locus, based on sequence, bin, and flanking markers
+ IBM2 2005 Neighbors
   Described below
+ IBM2 2005 Neighbors Frame
   Described below


Neighbors
+IBM neighbors v.2
   3,410 loci, frame is IBM1, computed by hand


+IBM2 neighbors

   5,696 loci, frame is IBM2, computed by algorithm


+ IBM2 2004 neighbors
   5,844 loci, frame is IBM2, refined by

   + IBM2FPC0402 genetic neighbors


IBM2 2005 neighbors
   34,581 loci, frame is IBM2, order refined by IBM2FPC0507, includes both genetic and BAC mapped loci


Genetic maps included:
IBM-94 maps: + IBM ISU Map4; + IBM GNP2004; + cIBM2005

IBM-302 maps*: + INDEL (MMP); +IBM1

SSR: + SSR Tx303xCO159 2002; + SSR T218xGT119 2002

BNL mapping population: + CU 99; + CU 98; + BNL 96 frame; + BNL 2002; + LHRF GNP*; + Genetic 2005; + MITE*;
*connotes very high resolution mapping panel

IBM2 2005 Neighbors Frame
   IBM2 2005 Neighbors loci that are all well-ordered (backbone, on frame, skeletal)