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MIT SNP Database

The Portable Dictionary of the Mouse Genome

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MIT Microsatellite Database ONLINE

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Chromosome Text Files from the Dictionary

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 Mouse Genetic Map Files

Updated Nov. 2, 2000

The following files are in text or Map Manager format. You can download Macintosh or Windows versions of Map Manager at the Map Manager QTX web site.

Many files have been bin-hexed (files with the ".hqx" suffix). You will need a decoding utility such as BinHqx or Stuffit Expander (available for Mac and Win) to decode Map Manager files. To configure your web browser to automatically launch a Map Manager file after downloading and decoding, add Map Manager as a helper application for the MIME type "application/x-mapmanager" and the file extension ".mm.hqx."


A Tenth Generation Advanced Intercross Map Manager files

    R.W. Williams and G. Zhou, November 2000 Update

  1. Genetic Maps based on a set of 500 10th generation progeny in a simple text format. The cross was generated starting with reciprocal intercrosses between the common strains C57BL/6J and DBA/2J. We crossed progeny for 10 generations, intentionally mating animals with as few common immediate ancestors as possible. This is why the progeny are referred to as Generation 10 (G10) rather than the Filial F10 generation. This 348 kb text file should be saved and then opened in Map Manager QTX, Excel, or a text-editing program. Each row consists of 7 fields that are separated by tab characters (tab-delimited). Each of the 340 rows has the following structure: CrossName tab Chromosome tab MarkerName tab Position tab 500Progeny tab Reference tab Notes. Empty fields actually contain a single period. Individual genotypes in the field of 500 progeny are delimited by single spaces and can be parsed into columns of a spreadsheet program such as Excel (select Data, then Text to Columns...). However, most spreadsheets, including Excel, DO NOT support more than 256 columns. (Sept 27, 2000, RW)

    For QGene users: Here are the two BDG10 text files that this Macintosh QTL mapping program needs to get going. This pair of files also includes a set of sample phenotypes that you can use to explore multiple trait mapping. The traits are: brain weight, eye weight, raw and residual weights of the hippocampus, olfactory bulbs, and cerebellum. The residuals were computed to minimize variance associated primarly with brain weight. Weights of the eye, brain, and brain parts are expressed in milligrams; body weight is expressed in grams. (November 2, 2000, RW)
    1. Map file
    2. Population file

    Genotypes were generated by Maggie Yin at the Mammalian Genotyping Service with the support of the NHLBI (Dr. James Weber, PI).



Recombinant Inbred Map Manager files

Composite High-Resolution RI Microsatellite Maps, Release 1, Jan 15, 2001

Release 1 of the Consensus Maps of RI Strains is described in a preprint included with the data release. RI consensus maps were assembled from genotypes of over 1500 microsatellite loci by R. Williams and colleagues (Informatics Center for Mouse Neurogenetics).

Complete BXN Database in Map Manager QTX-style text format: 853 KB datafile (inferred genotypes)
Complete BXN Database in native Map Manager QTXformat: 772 KB datafile (inferred genotypes)
Complete BXN Database in graphic format: 1.9 MB GIF image file format for printing or reformating in Photoshop (wall paper format).

Table 2

    R.W. Elliott, 1997 edition

  1. AXB/BXA RI data
  2. AXB/BXA QGene population text file (RWiliams, Nov 2000 data)
  3. AXB/BXA QGene map text file (RWiliams, Nov 2000 data)
  4. AXB/BXA RI data for QTL analysis
  5. BXD RI data
  6. BXD RI data: Truncated to 584 loci with unique strain distribution patterns: for QTL mapping
  7. AKXD RI data
  8. AKXL RI data
  9. BXH RI data
  10. BXJ RI data
  11. CX8 RI data
  12. CXB RI data
  13. CXJ RI data
  14. CXS RI data
  15. LSXSS RI data
  16. LXP RI data
  17. NX8 RI data
  18. NX9 RI data
  19. NXSM RI data
  20. OXA RI data
  21. SWXJ RI data
  22. SWXL RI data
  23. 129XB RI data
  24. 58NXL RI data
  25. 9XA RI data
  26. BRX58N RI data


MIT F2 Intercross Panel Data Files

These files were generated from the Whitehead/MIT Center for Genome Research SSLP F2 panel, Release 9 (April 1995) by R.W Williams. All chromosome-specific files are under 80 KB.


  1. MIT loci, Chr 01
  2. MIT loci, Chr 02
  3. MIT loci, Chr 03
  4. MIT loci, Chr 04
  5. MIT loci, Chr 05
  6. MIT loci, Chr 06
  7. MIT loci, Chr 07
  8. MIT loci, Chr 08
  9. MIT loci, Chr 09
  10. MIT loci, Chr 10
  11. MIT loci, Chr 11
  12. MIT loci, Chr 12
  13. MIT loci, Chr 13
  14. MIT loci, Chr 14
  15. MIT loci, Chr 15
  16. MIT loci, Chr 16
  17. MIT loci, Chr 17
  18. MIT loci, Chr 18
  19. MIT loci, Chr 19
  20. MIT loci, Chr X
  21. MIT loci, All Chromosomes � 1.4MB

Jackson Lab Backcross Panel Map Data

The following two files were provided by Lucy Rowe of theJackson Laboratory (see Rowe et al. (1994) Mammalian Genome 5:253). Please contact Lucy Rowe ( or Mary Barter ( if you have specific questions regarding either dataset. These datasets were obtained Feb. 1996.


Shionogi Loci

The following three files were provided by V. Chapman and K. Manly, Roswell Park Institute. A paper describing these loci is now in press. Please contact Drs. Chapman and Manly if you have specific questions regarding these files.


Copeland-Jenkins-MIT map � 246 KB

This Map Manager file includes the data that were used to generate the poster "Genome Maps IV, The Mouse." This poster accompanied an article by Copeland et al (1993, Science 262:57-66) entitled, "A genetic linkage map of the mouse: Current applications and future prospects." This Map Manager file includes data on 912 loci typed in a group of 203 interspecies backcross animals (C57BL/6JxSPRET/Ei)xC57BL/6J.

The order of loci and their positions were fine-tuned by R. Elliott. The nomenclature has been updated and corrected by R. Williams. As explained in detail below, the order and positions of loci in the Map Manager file may differ somewhat from those on the Genome Maps IV poster.


Copeland-Jenkins-MIT map data

Notes on this Map Manager file by R. Elliott and R. Williams (March 10, 1994)

The original file was obtained from the Center for Genome Research via anonymous ftp at Nomenclature of loci was brought into concordance with the Portable Dictionary of the Mouse Genome. The file was transferred to Microsoft Word, reformatted, and imported into Map Manager 2.5.

Once in Map Manager, the ends of each map were anchored using proximal and distal loci that were shared between the Mouse Chromosome Committee Reports and the Copeland/Jenkins backcross panel. Loci typed by Neil Copeland, Nancy Jenkins, and their co-workers were ordered in sequence, working from the ends toward the middle of each map. The "Links Report" feature of Map Manager�set at 99.99% probability�was used to position loci with the highest LOD scores. Other loci were added and ordered using internal recombination data. The process was repeated until the loci overlapped in the middle of each map. The MIT SSLP marker loci were added next. These microsatellite loci were moved in groups that shared similar progeny distribution patterns (PDPs). The "Links Report" feature was used again, and sets of loci with similar PDPs were again shifted and reordered. Following this integration between the two types of loci, the data set was reexamined to find all single locus double recombinants. The order of loci was adjusted.

A DISTANCE CAVEAT: The map distances given in the map window of Map Manager differ somewhat from those published on the Genome Maps IV poster. These Map Manager position estimates do not take into account obligate crossovers that are not completely defined. However, the map distances in the haplotype window of Map Manager do take these crossovers into account, and consequently, the distances given in this window often differ from those in the map window. (The haplotype window splits the difference on the undefined crossovers, assuming that the recombination event occurred in the middle of the interval.)

A third distance estimate may be obtained by using the "infer phenotypes" feature in Map Manager. Note however, that this "infer phenotypes" feature was developed for maps that use completely typed anchors. In this Fredrick-MIT dataset the anchors are not established and the recombinant animals were often not typed for the loci on either side of the crossover. (The choice of animals to be typed probably varied between loci and was apparently based on other criteria.) Thus using "infer phenotypes" skews the data in favor of non-recombinants, giving a low estimate of the distance. In contrast, the data used in the map window in which phenotypes are not inferred may be skewed the other way for some of the loci.


Neurogenetics at University of Tennessee Health Science Center

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