<p>I am using 1000 Genomes data with my new project. 
When I am inspecting the reference assembly they have been using, I found it contains a "decoy" contig. </p>

<p>The <a href='http://www.1000genomes.org/faq/which-reference-assembly-do-you-use'>1000 Genomes FAQ</a> says:</p>

<blockquote>
  <p>For the final round of alignments the sequence data will be mapped to
  a set of sequences derived from the GRCh37 assembly.  This
  GRCh37-derived alignment set includes chromosomal plus unlocalized and
  unplaced contigs, the rCRS mitochondrial sequence (AC:NC_012920),
  Human herpesvirus 4 type 1 (AC:NC_007605) <strong>and decoy sequence derived
  from HuRef, Human Bac and Fosmid clones and NA12878</strong>. These files are
  available in phase2_reference_assembly_sequence on the ftp site.  All
  human variant coordinates reported by the 1000 Genomes project are in
  GRCh37 coordinates.</p>
</blockquote>

<p>Here, I have no idea what the decoy sequence is and why it is included. Maybe to detect sample contamination?</p>

<p>The reference genome is incomplete, particularly around the centromeres, so often reads which truly belong elsewhere are wrongly mapped to a particular place in the genome because the true match is missing from the reference. These cause false positive calls, which were bothering us in the 1000 Genomes Project. The decoy is a pragmatic solution to this - it contains known true human genome sequence that is not in the reference genome, and will "suck up" reads that would otherwise map with low quality in the reference. The decoy was built by Heng Li, at the Broad, working with Richard Durbin (Sanger) and Deanna Church of the Genome Reference Consortium (who maintain the reference genome).</p>
