Gap (AGP defined) Track Settings
AGP gap   (All Mapping and Sequencing tracks)

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This track shows the gaps in the 07 Dec 2012 Microtus ochrogaster/GCF_000317375.1_MicOch1.0 genome assembly.

Genome assembly procedures are covered in the NCBI assembly documentation.
NCBI also provides specific information about this assembly.

The definition of the gaps in this assembly is from the AGP file: GCF_000317375.1_MicOch1.0.agp.gz
The NCBI document AGP Specification describes the format of the AGP file.

Gaps are represented as black boxes in this track. If the relative order and orientation of the contigs on either side of the gap is supported by read pair data, it is a bridged gap and a white line is drawn through the black box representing the gap.

This assembly has 180,558 gaps, with the following principal types of gaps:

  • scaffold - gaps between scaffolds in chromosome assemblies (count: 180,558; size range: 100 - 40,662 bases)