Rapid haplotype inference for nuclear families

Table 4 Four types of loci Hapi distinguishes

			Number of states
Locus type	Parent p	Parent q	If sprevious states	Average
Fully informative for both parents	a/b	a/c or c/d	1	N/A
Fully informative for one parent	a/b	a/a or c/c	After informative for parent q: 1 Previous states unambiguous: ≤s Previous states ambiguous: ≤2s	1.87
Partly informative	a/b	a/b	≤4s	6.31
Uninformative	a/a	a/a or b/b	0	N/A

The four types of loci our algorithm handles separately with the names we use to refer to them. The table lists the number of states that Hapi produces for each type if there are s states at the previous locus, and gives the average number of states produced for haplotyping the dataset we evaluate in Results. Note that either parent may have the genotypes listed for parents p and q.

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