Understanding "Black Reads"

[Mélyyy]

Hi everyone,

I'm currently visualizing some Long-Read sequencing data (Nanopore) in IGV and I'm seeing several reads appearing entirely in black/dark grey. (picture for reference)

I've looked into the read details for one of them, and here is what I found:

• Mapping: Secondary @ MAPQ 0

• Flags: 272 (Not primary alignment + Reverse strand)

•     Read Length: 37,138 bp

•  Reference Span: ~7,300 bp

•  CIGAR/Clipping: Massive soft-clipping (approx. 29,700 bp on the left).

I understand that "black" usually denotes a Mapping Quality of 0 or a secondary alignment but usually they're white or colored if they're are soft-clipped, but I'm trying to figure out why such a large portion of a 37kb read is soft-clipped while the rest is mapped here on chr20.

•  Does this usually indicate a segmental duplication or a structural variant (translocation/chimerism)?

• Is there a specific setting in IGV to easily jump to the Primary Alignment for this specific Read ID?

• Should I be concerned about these reads for variant calling, or is it safer to filter out all flag 256 reads?

Any insights into the "black read" behavior in IGV for long reads would be greatly appreciated! 

Thank you in advance.

Mélissa