Furthermore, we correct IBD segment lengths for IBD with archaic genomes, as archaic genomes only match a part of the IBD segment that is shared among humans. The raw lengths were computed as the length of the maximal IBD sharing between two individuals that possess the IBD segment. This resulted in overestimation of the lengths, which are corrected as described below.
We are interested in IBD between human and archaic genomes. However, the human IBD segment length is not an appropriate measure for the length of IBD with archaic genomes because only a part of the IBD segment may match an archaic genome (see Figures 33, 34, and 35).
We correct the IBD segment lengths to obtain the IBD lengths between human and archaic genomes. The corrected length of an IBD segment is the length of the ``archaic part'' that matches a particular archaic genome. First, the left (upstream) break point of the ``archaic part'' of an IBD segment genome is detected. This left break point is defined as the first location in the IBD segment from the left (upstream), where at least 4 out of 9 tagSNVs match the archaic genome. From the right (downstream), the right break point of the ``archaic part'' of an IBD segment was detected analogously. Since not all bases of the Neandertal genome were called, we modified the definition of the break points. For the Neandertal genome, a break point requires at least 5 or 6 bases of the 9 tagSNVs to be called of which 2 or 3, respectively, have to match the Neandertal genome. If either the left or right break point of an ``archaic part'' could not be found, then this IBD segment does not contain an ``archaic part''.
Matching of an IBD segment and an archaic genome for IBD segment lengths analyses was defined as: