No Illumina Results
No Large Deletions
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).