Annotations for the Mouse Diversity Array for the reference sequence and 14 Sanger strains
See Didion et al. 2012 (BMC Genomics) for details on how these files were generated.

General notes:
* If a probe has an alignment score < 0 (column #9 below), there will be no data in
any subsequent column.
* All position are given in terms of 5'-3' orientation of the forward strand, regardless 
of the orientation in which the probe mapped.
* Imputed sequence annotations are given in the coordinates of the imputed sequence.
* Columns that are only in the reference strain annotations are marked with an asterisk ('*').
  Columns that are only in the imputed strain annotations are marked with a plus ('+').

Columns:
  1. SNP/Probeset ID ('JAX' followed by an eight-digit number).
  2. The originally annotated reference sequence base of this SNP.
  3. The originally annotated variant base of this SNP.
  4. The SNP's substitution type (transition or transversion).
  5. The originally annotated probe orientation. There will always be two records for each
     probe set, one in the forward orientation (+) and one in the reverse orientation (-). 
  6. Alignment score:
      -3 = Non-unique probeset: No probe in the probeset aligned uniquely
      -2 = Unaligned: The probe failed to align with <= 1 mismatch
      -1 = Non-unique probe: This probe aligned equally well to more than one location in the genome,
           but other probes in the probeset aligned uniquely
       1 = Mismatch: The probe aligned uniquely with 1 off-target mismatch
       2 = Perfect: The probe aligned uniquely with no off-target mismatches
  7. The IDs of the probes that map to this strain. There are eight probes on the array for every
     SNP probe set (two replicates each of four different sequences):
       * 2 for the reference allele in the forward orientation
       * 2 for the variant allele in the forward orientation
       * 2 for the reference allele in the reverse orientation
       * 2 for the variant allele in the reverse orientation
     So the two IDs in this column (comma-delimited) are of the two probes that best align to the
     genome of this strain of the four originally annotated to be in the same orientation (column #5).
  8. Probe base: The target base of these probes.
  9. Probe sequence: The genomic sequence these probes were designed to interrogate.
 10. Suboptimal alignments: Number of alternative alignments of lower quality than the best alignment.
 11. Chromosome: The chromosome to which the probe mapped. Probes from the same probeset may be
     mapped to different chromosomes.
 12. Target physical position (in bp): The physical position to which the target (polymorphic) 
     base mapped.
*13. Target genetic position (in cM): The genetic position to which the target (polymorphic) 
     base mapped. This is a sex-averaged position, and is not defined for chromosomes Y or M.
 14. Target base: The nucleotide at the target position in the genomic sequence. 
 15. Target rsID: The rsID of the SNP at the target position.
 16. Target deleted: 0 = The polymorphic base in the probeset (the position intended to interrogate
     the SNP in the genomic sequence) has been deleted in the genome sequence; 1 = no deletion.
 17. OTV position: If the alignment score = 1, the position of the OTV (off-target variant).
 18. OTV type: s = SNP, i = insertion, d = deletion
 19. OTV probe base: The nucleotide at the OTV position in the probe. This will always be a single
     base unless the OTV type is 'i', in which case it will be empty
 20. OTV target position: The nucleotide at the OTV position in the genomic sequence. This will 
     always be a single base unless the OTV type is 'd', in which case it will be empty.
 21. OTV rsID: rsID (if any) of the OTV.
 22. Orientation: The orientation in which the probe mapped (+ or -).
 23. Probe start position: Physical position to which the first base of the probe mapped.
 24. Probe end position: Physical position to which the last base of the probe mapped. 
 25. Target sequence: The genomic sequence to which the probe best aligns. This is identical to 
     column #9 when the alignment score = 4 and probe base = target base. Undefined for 
     chromosome M.
 26. Probe C/G fraction [0-1]: Fraction of bases in the probe that are C or G.
 27. SNP source: See Yang 2009 for a description of the different data sources used to design the 
     array.
 28. NspI proximal position: proximal (starting) position of the NspI fragment containing this probe.
 29. NspI distal position: distal (ending) position of the NspI fragment containing this probe.
 30. NspI C/G fraction [0-1]: Fraction of bases in the NspI fragment that are C or G.
 31. StyI proximal position: proximal (starting) position of the StyI fragment containing this probe.
 32. StyI distal position: distal (ending) position of the StyI fragment containing this probe.
 33. StyI C/G fraction [0-1]: Fraction of bases in the StyI fragment that are C or G.
*34. ENSEMBL gene IDs: ENSEMBL ID(s) (comma-delimited) of the gene within which this probe aligns 
    (if any).
*35. Function: Functional annotation of the gene within which this probe aligns (if any).
+36. Target coverage depth: 0 = the coverage depth was below the threshold, 1 = the coverage depth
     was above the threshold.
+37. Target sequence low coverage: Number of bases in the probe for which the genomic sequence had
     below-threshold coverage depth.