The key to understanding SOIiD technology is to understand the labeled oligo mixture.  The probe is an 8-mer oligo which has a fluorescent dye labeling on its 5’ end. After the annealing of a primer, ligase will ligate a labeled probe, whose first two nucleotides are complementary to the template to the primer.  When the image collection finishes, the last 3 nucleotides and its fluorescent dye are cleaved, leaving 5-mer oligo attached to the template.  While the ligation repeats, as shown in the first row of step 8 above, nucleotide positions at 1, 2, 6, 7, etc. are read once.  In order to read the spaces that have not been read after this first extension, the extended fragments are melted away and a new primer, with a  one-base shift toward the bead, is annealed to the template (this is called primer reset), and a new ligation cycle begins.  To   read the sequencing in its entirely, 5 rounds of primer annealing are necessary. 

Each probe detects two nucleotides simultaneously and there are 16 probes available to cover all of the possible di-nucleotide combinations; , there are only 4 dyes  available for labeling and here is how the so- called color space and sequencing are connected.

As displayed above, if the first nucleotide and second nucleotide are both A, then the blue dye is used to label that probe.  Each dye represents 4 di-nucleotide probes. As we saw earlier, for each nucleotide position in the sequence, it will be read twice during ligation, which generates two color spaces.  By using these two color spaces, a nucleotide can be determined.