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Percentage of N bases

Category Annotation Modules

VCF Field INFO (variant-level)

Header definition line
  • INFO=<ID=PercentNBase,Number=1,Type=Float,Description="Percentage of N bases in the pileup">

  • Overview

    N occurs in a sequence when the sequencer does not have enough information to determine which base it should call. The presence of many Ns at the same site lowers our confidence in any calls made there, because it suggests that there was some kind of technical difficulty that interfered with the sequencing process.


    In GATK versions 3.2 and earlier, this annotation only counted N bases from reads generated with SOLiD technology. This functionality was generalized for all sequencing platforms in GATK version 3.3.

    Related annotations

    • BaseCounts counts the number of A, C, G, T bases across all samples.

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    GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.