definition of chimeric vs multiple-mapping (SAM)

Question

[Pfs]

I would like to understand better the difference from a chimeric alignment and a multiple-mapping alignment. From the information in the SAM specifications, it seems to me that a chimeric alignment takes place when the part of the query read can map to different places in the reference sequence, whereas a multiple-mapping alignment takes place when the whole query read can map to different places in the reference sequence.

Thus, a read can be chimeric if parts of the reads map to the same chromosome but in different places?

Thanks in advance.

Answer 1

[Devon Ryan]

Correct, a chimeric (or "non-linear") alignment occurs when non-overlapping portions of it map to (A) different portions of the same chromosome in a manner not normally biologically supported or (B) to different chromosomes. Multimapping occurs commonly in repeat regions or where there are paralogs. Chimeric alignments occur when there are structural rearrangements, such as with cancer (or something weird happened during sample preparation).

[Dunois]

Could you clarify what "non-overlapping portions" is supposed to mean in this context?