Proportion of Reads

Assigned Types By Read Alignment Characteristics

Single-Stranded vs Self-Complementary Frequency

Assigned AAV Types

Flip/Flop configurations, scAAV only

Flip/Flop configurations, ssAAV only

AAV Sequence Length by Type

AAV Mapping to Reference Sequence

Coverage Over Regions of Interest

Sequence Annotations

Sequence Variants

No Illumina Results

Number and Frequency of Sequence Deviation from Design (Variants)

Length Distribution of Deletions

No Large Deletions

Human Alignments Distribution

Human Gene Count

Appendix

Type Subtype Definition
ssAAV full Read consists of a DNA sequence which includes the entire ITR-to-ITR target vector sequence. Read is present only in either (+) or (-) polarity.
ssAAV left-partial Read consists of a fragment of the vector originating from the upstream (left ITR) of the vector while not covering the right ITR. Read is present only in either (+) or (-) polarity.
ssAAV right-partial Read consists of a fragment of the vector originating from the downstream (right ITR) of the vector while not covering the left ITR. Read is present only in either (+) or (-) polarity.
ssAAV partial Read consists of a fragment of the vector originating from within the ITR sequences. Read is present only in either (+) or (-) polarity.
ssAAV vector+backbone Read consists of a fragment including the vector as well as plasmid backbone sequence. Read is present only in either (+) or (-) polarity.
ssAAV backbone Read consists of a fragment originating solely from the plasmid backbone sequence. Read is present in both (+) or (-) polarity.
scAAV full Read consists of a DNA sequence which includes the entire ITR-to-ITR target vector sequence. Read is present in both (+) and (-) polarities.
scAAV left-partial Read consists of a fragment of the vector originating from the upstream (left ITR) of the vector while not covering the right ITR. Read is present in both (+) and (-) polarities.
scAAV right-partial Read consists of a fragment of the vector originating from the downstream (right ITR) of the vector while not covering the left ITR. Read is present in both (+) and (-) polarities.
scAAV partial Read consists of a fragment of the vector originating from within the ITR sequences. Read is present in both (+) and (-) polarities.
scAAV vector+backbone Read consists of a fragment including the vector as well as plasmid backbone sequence. Read is present in both (+) and (-) polarities.
scAAV backbone Read consists of a fragment originating solely from the plasmid backbone sequence. Read is present in both (+) and (-) polarities.
unknown/other NA Read consists of a fragment mapping to the vector but with unexpected polarities (e.g. +,-,- or +,+,+) and cannot be well-defined at the moment. Usually this means there’s multiple supplementary alignments on the vector region or and it’s a weird molecule.
host NA Read originates from the host genome that is given (e.g. hg38, CHM13).
repcap NA Read originates from the repcap plasmid. The Rep gene encodes four proteins (Rep78, Rep68, Rep52, and Rep40), which are required for viral genome replication and packaging, while Cap expression gives rise to the viral capsid proteins (VP; VP1/VP2/VP3), which form the outer capsid shell that protects the viral genome, as well as being actively involved in cell binding and internalization.
helper NA Read originates from the helper plasmid. In addition to Rep and Cap, AAV requires a helper plasmid containing genes from adenovirus. These genes (E4, E2a and VA) mediate AAV replication.
chimeric NA Read consists of fragments that map to one or more "genomes" (e.g. vector and host; helper and repcap)

"A read is "scAAV" if it has both a primary and supplementary alignment to the vector genome. Subtype classification follows the ssAAV example.

Note that even though ssAAV distinguishes one ITR as the wildtype (wtITR) and the other as the mutated ITR (mITR) we will still refer to them as leftITR vs rightITR (so using "left-partial" which in this case would be equivalent to saying "mITR-partial" since the mITR is the left IT based on the genomic coordinates given here).