Column descriptions of the variants file (Final.Variants.140604.xls)

The variants data reported in this file consist of four elements describing the polymorphism:
      • identifier
• unique coordinate
      • strain distribution pattern (SDP)
• flanking sequence 

Below is a more detailed explanation of each element.

Column 1 (/Name/):
This column indicates the primer identifier or the gene in which the polymorphisms were found. If the variant is rare, then the name is followed by an asterix (/Name*/). In total, we identified 17 rare polymorphisms.

Column 2 (/Coordinate/):
The number in this column is unique and localises the polymorphism point in our complete BAC-based contig of 4,785,409 bp. 

Column 3 to 10 (/A/J, AKR, BALB/c, C3H, C57BL/6, DBA, I, RIII/)
These 8 columns contain one of the 4 nucleotides (A, T, C or G) to annotate SNP, I or D for insertion deletion polymorphism or a number indicating a repeat polymorphism.
For adjacent SNPs (27 in total), these columns contain more than one nucleotide, 22 rows with 2 nucleotides, 4 rows with 3 nucleotides and 1 row with 4 nucleotides.

To facilitate reading the SDP, a colour code system was adopted where strains with the same SNP were similarly coloured. We used grey for all groups that contain the reference strain C57BL/6, others were in pink. In/Del and diallelic repeat polymorphisms were treated the same way.  Different colours (purple, yellow, orange, green and blue) were used if repeat polymorphisms felt into more than 2 groups.

Column 11 (/5’ and 3’ flanking sequences/)
The nature of the polymorphism is indicated between square brackets, and on the left and right hand side of the brackets, respectively the sequence 5’ and 3’ to the site of mutation is displayed. 
- If a SNP, each of the alternative within the brackets is separated by a back slash, with the C57BL/6 alternative always on the right hand side of the slash.
- If In/Del and repeat polymorphisms, the nucleotides which are deleted, inserted or repeated are indicated.
- If long insertion deletion polymorphisms (3 cases in total), a number of base pairs is displayed within the bracket which indicates the length of the insertion or deletion.

The length of the flanking sequences is variable, the minimum being 40 base pairs.

Note:
For single nucleotide repeat polymorphisms, we used a threshold of 4 base pairs, below which we will annotate the variant as In/Del polymorphism.