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After having performed an alignment using bowtie2 and GRCh38 as a reference sequence, I got inusual matches on chrUn. Here a small part of the SAM file:

@SQ     SN:chr22   LN:50818468
@SQ     SN:chrX    LN:156040895
@SQ     SN:chrY    LN:57227415
@SQ     SN:chrM    LN:16569
@SQ     SN:chrUn_KI270424v1     LN:2140

All the other chr values are clear to me (M indicates the Mitochondrial DNA, while 22, Y and X are just the usual chromosomes number/name) but I couldn't figure out what chrUn stands for and what about that code after the _?

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    $\begingroup$ Usually "Unknown". Sequences that have not been assigned to one of the chromosomes. I think this is from the Human genome, which has multiple sequences not assigned to a chromosome, so they have identifiers (the KI...) $\endgroup$ – skymningen Apr 24 '17 at 9:17
  • $\begingroup$ @skymningen Thank you. If you add a reference and post it as an answer I will accept it. $\endgroup$ – alec_djinn Apr 24 '17 at 9:45
  • $\begingroup$ There is no reference for this, other than experience, sorry. $\endgroup$ – skymningen Apr 24 '17 at 10:01
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I presume chrUn_KI270424v1 refers to a scaffold or sequence that has not yet been assigned to a chromosome. The designation after the Un (unknown or unassigned?) may refer to a particular single sequence or a scaffold. You will be able to determin this by examining the reference sequence and its documentation.

(My assumption is based on the sort of thing one finds in the various versions of Drosophila reference genomes, with which I am familiar. So I can’t help you with the specifics of the human genome.)

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It is for unassigned sequences. See this reference from the UCSC Genome Browser FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download11

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