2. Example Amplicon Project Design and Analysis
:
2.5 Important Factors in the Assessment of New Variants
: 2.5.6 Read Length
2.5.6
Read Length
Sequencing quality can begin to drop off at the trailing edge of a read. You should closely examine potential Variants that are at the edges of reads. On the alignment tabs, the orientation of the reads with respect to the reference is indicated, so the end of a forward read is to the right and the end of a reverse read is to the left. If your Variant is at the end of a forward or reverse read, you should examine other types of corroborating factors like bidirectional support and flowgram evidence. If your candidate Variant only has support in a single direction, you should look at multiple reads in the same direction that share the Variant of interest. If the reads have multiple additional errors in close proximity to the Variant, it is likely an indication that the Variant isn’t real but is the result of read quality drop off.
