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The Genome Browser offers several ways to highlight gaps in alignments of query sequences (usually transcripts) to the genome. Gaps result from sequences in the genome or query (or both) that cannot be aligned.
When zoomed out past the base level, the browser chooses one color to represent many bases. The priority of display, from most important to least important, is: different mRNA base/nonsynonymous codon coloring (if enabled) or different item bases (if enabled), unalignable query sequence (orange or purple), an insertion in both genome and query (double horizontal line), and a poly-A tail (green). The browser will not display genomic/mRNA codon coloring when viewing large regions of the genome.
Interpretation of Display
Gaps are usually due to a deletion or insertion in one or both sequences, or, infrequently, a problem in the sequencing. Often, the genome will have a large "insertion" relative to a query (single horizontal line) that is actually an intron. Double-sided insertions (double horizontal line) are unusual and may indicate an assembly error, sequencing error, or polymorphism.
Unalignable query sequence in the middle of a query (orange) implies extra bases in the transcript sequence or missing bases in the genome sequence. Insertions at the beginning or end of a query (purple), implies a partial alignment of the query. For instance, a very short sequence next to large intron gap may be incorrectly aligned. Unalignable query sequence may also be due to polymorphisms.
Poly-T heads result from queries that are the reverse complement of the genomic sequence. Poly-A tails and poly-T heads (green) of mRNAs usually can not be aligned to the genome; this is a special case of an unalignable query sequence.