In order to understand this section you will need an understanding of basic genetic terms, what alleles are dominant over others, what genes are epistatic to others (the Genes page can help with this), etc. In order to apply what is taught here into your breedings, you need to understand what genotypes your mice are. Punnett Squares are only as accurate as the information you put into them.
Each baby inherits one allele on each locus from each parent. Below I will explain how to make a punnett square, which will aid you in determining what alleles a given litter will inherit from their parents, making all possible genotypes for a given locus. This punnett square only covers one locus. Following chapters will cover more than one.
For the sake of example, I'm going to do a punnett square for a Heterozygous Agouti Father A/a and a Heterozygous Lethal Yellow Mother Ay/a.
To make a punnett square for one locus you need to draw a table that has 3 rows and 3 columns like the one below.
The top left square is always left blank.
Next fill in the alleles for each parent. In the top row add both alleles, one per square, for the father (shown in the blue squares). On the left side column add both alleles, one per square, for the mother (shown in the pink squares). When listing the alleles, make sure that you place the dominant allele first. In the case of both alleles being dominant, add the one that is dominant over the other first.
Next we start filling in the middle squares which will determine what combinations of alleles the offspring can inherit for that locus. Start with the first open square. To do this with the most accuracy, you should always add the more dominant allele first. For the first square you take the Ay from the mother (directly to the left of the purple square you are filling in) and the A from the father (directly above the square you are filling in) and add them to that first open square, as shown below.
You will fill in each additional square the same as you did the first. Take an allele from each father and mother to fill in the corresponding square.
To fill in the second square, take the Ay from the mother and the a from the father.
Second row, first square; fill in the A from the father and the a from the mother.
Last square; fill in the a from the mother and the a from the father.
Here we can see all of the possible combinations of alleles the babies can inherit (in purple). There are 4 possible combinations of alleles that the litter can inherit on that locus. Basing it on the laws of statistics, Each square accounts for 25% of your litter. You should get 25% of each Ay/A, Ay/a, A/a, and a/a.
Now that you know what combinations of alleles the offspring can inherit on that locus, you can partially determine what the babies will look like (phenotype). Statistically you get: 25% Agouti (A/a genotype). 25% Non-Agouti (a/a genotype). 50% Lethal yellow (both Ay/a and Ay/A genotypes will give you Lethal Yellow Phenotype because Lethal yellow is epistatic to Agouti). Note that when you factor in other alleles on other loci, the phenotype may be significantly different than what you see when only factoring in only one locus.
Next: Inheritance, Punnett squares ~ 2 Loci