Haplotype extension. Haplotype extension proceeds from the lower index to the higher index. (A) Haplotypes can extend over more than four strongly potential polymorphisms as the result of the previous haplotype extension. We assume that the extended haplotypes, · · · CCTAA and · · · ATCCT, are given up to the (i + 3)-th position. (B) After the local haplotypes, AACA and CTGT, are obtained in (1), the extended haplotypes in A can be combined with the local haplotypes and extended to · · · CCTAACA and · · · ATCCTGT by the consistency of shared strongly potential polymorphisms (the dashed box) at the (i + 2)-th and (i + 3)-th positions. The combined haplotypes are shown in (2). (C) In (1), an inconsistency is observed at the (i + 2)-th position. After the local haplotypes are extended to the (i + 1)-th position, the inconsistency is resolved in (2). The combined haplotypes are shown in (3). (D) Although the local haplotypes are extended in (2), the inconsistency at the (i + 2)-th position is still observed. The number of matches for two phases is calculated from the (i + 1)-th to the (i + 3)-th position (in the dotted box): in this example, 5 for one direction of connection and 0 for the other direction of connection. The resolved extension is shown in (3).
