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The sequence of the reference genome is added to the Chromosome view by default, as long as it has been added to the respective genome on the Library File Management page. However, its presence (or absence) in the viewer depends on the current magnification. At low power, the track is hidden and you will see the message - Track hidden (zoom to view). At high power, on the other hand, the Reference genome track becomes visible (Figure 32) and is supplemented by the genomic coordinates (below the sequence). A vertical guide helps you to align the bases between Aligned reads and Reference genome tracks. Depending on the reference genome file, some bases may be shown in lowercase letters, symbolizing repetitive sequences, or other sequences masked by a tool such as RepeatMasker.

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