Fig. 4.

The figure shows how the human segment of a read may be unaligned by BLAST. The black and gray lines indicate the human and viral reference genomes, respectively. The red segments are sequences originating from viral genome and the blue segments originate from the human genome. The green segment indicates a random sequence and the blue vertical lines indicate places where reference and the human segment match. In (1), although the human segment matches the reference, it is too short to be detected by BLAST. In (2), a random sequence is present in the integration and the human segment present is too short to be detected by BLAST. In (3), their is no human segment at all. This may be due to an insertion or due to a misalignment of the sequence. We will attempt to rescue reads in cases (1) and (2) through local alignment