An example of false positive resulting from a paralog sequence. (A.) Multiple alignment of RNA-seq reads and genomic DNA (maternal and paternal genome) Note: only part of the RNA reads mapping to the position are shown here. (B.),(C.) BLAST results of the alignment of the genomic version of the sequence to the reference genome (NCBI build 37). It can be aligned to the reference genome at more than one position. The gap highlighted in (C) by the red rectangle is the same as the indel difference shown in (A).
Chen and Bundschuh BMC Genomics 2012 13:616 doi:10.1186/1471-2164-13-616