Identification of a deletion within the WHSC1L1 gene. (A, B) Alignment of the read 1B with the corresponding genome regions of WHSC1L1. Splice junction nucleotides are indicated in red. (C) Schematic representation of the putative intragenic deletion, (probably due to a looped transcript) in WHSC1L1, identified by the read 1B. The green and blue arrows represent the two halves of the fusion transcript which map on the opposite order to the genome.