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Converting a Single Value

The Single Conversion form provides an easy way to convert a single position from a selected input format to a selected output format. When the input format is selected an example of the correct syntax will be shown next to the input text box. If conversion fails, an error message will be displayed describing the error.

Batch Conversion

Batch conversion has the same basic functionality as the single position conversion tool except that you can convert a number of positions at the same time by uploading a data file or by pasting text into the text box, clicking the convert button and downloading the results link. In order to format your data correctly:
  • Use spaces or tabs to separate data columns
  • For base pair and centimorgan inputs the second to last column is the chromosome number and the last column is the position. For MIT marker inputs the last column is the marker name and for all of these input formats any earlier columns are ignored.

Here are some examples of correctly formatted input data:
  • Centimorgan input: 
    1 44.4
2 3.2234
1 77
5 44.21
6 21.1
4 19.002
1 55
  • Centimorgan input with a single column of ignored data: 
    anything 1 44.4
that     2 3.2234
I        1 77
put      5 44.21
here     6 21.1
is       4 19.002
ignored  1 55
  • Base pairs: 
    1 92887845
2 7821365
1 172956646
5 92572826
6 47433029
4 41364422
1 131246731
  • MIT markers: 
    D11Mit304
D11Mit16.1
D11Mit16
D11Mit16.2
D5Mit143
D5Mit102
D6Mit231
  • SNP ID's (RS#'s or JAX SNP ID's): 
    rs3675244
rs3711314
rs3023460
rs3707114
rs3706767
16-088616314-G
M-01322_2
16-090091107-C

When you view the text or HTML formatted output of a batch conversion, you will see a status indicator such as "SUCCESS" or "CHROMOSOME_NUMBER_OUT_OF_BOUNDS". Here's how you can interpret each of these codes:
  • SUCCESS: the input was successfully mapped to the output coordinates using the preferred methodology.
  • CHROMOSOME_NUMBER_OUT_OF_BOUNDS: the position could not be mapped because the chromosome number of the input is not valid for the chromosome number of the output. Typically this is because you are trying to convert chromosome 20 to the sex averaged or male centimorgans output.
  • UNKNOWN_SNP_ID: the given SNP Identifier is not contained in this application's database. This is often caused by a typo.
  • UNKNOWN_MIT_MARKER: the given MIT Marker is not contained in this application's database. This is often caused by a typo.
  • MISSING_PRIMER_SEQUENCE: the primer sequence could not be identified for the given MIT Marker.
  • UNMAPPED: failed to map given MIT Marker to a physical position on the genome.
  • MAPPED_TO_MULTIPLE_LOCATIONS: the given MIT Marker has been mapped to more than one location on the genome.
In the case of MIT Markers we can sometimes provide an output position even if the status is not "SUCCESS". This is done by either using MGI's database or, in the case of multiple mappings where the difference between positions is less than 1 Mb, the mean of the mapped starting positions is used. In either case, the method will be explained by a note in the last column of the output.

Please send questions or comments to mousemapconverter@jax.org

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