How do I Interpret the Align to Reference Map View?

In Map view, after performing an alignment to reference, the position and orientation of each aligned sequence is represented as an arrow above the reference sequence.

Aligned sequences that are selected in the side panel are colored blue. Unselected reads are colored dark red.

1. A filled colored region (dark red or blue) indicates a perfect match between the aligned reference and the read in that region.
2. A white area at the 3' end of the read indicates the region has been hidden due to lack of similarity to the reference sequence. The lack of similarity may be due to legitimate differences between the sequences, or due to low quality of the aligned sequence in that region (if an aligned .ab1 or .fastq trace file).
3. A white area at the 5' end of the read indicates the region has been hidden due to lack of similarity to the reference sequence. This is usually due to low quality base calls at the beginning of the aligned ab1 or .fastq sequence, but it may also indicate a lack of similarity to the reference sequence.
4. A white area within the aligned region indicates either a mismatch between the reference and the aligned sequence at that position, or a deletion within the aligned sequence at that position.
5. A vertical line or a triangle above the arrow indicates an insertion of 1 or more nucleotides in the aligned sequence that are not present in the reference sequence.

See Align Sanger Reads to a Reference Sequence to learn how to view and validate your aligned sequences.