Missing supplementary alignment display for contig in IGV

[biorococo]

Hi,

I am visualising an assembly aligned to hg38 in IGV v2.19.7 and I can't see an expected supplementary alignment.

The contig has the following supplementary alignments:

Supplementary Alignments
chr7:107,771,965-108,418,959 (+) = 646,996bp @mapq 60 NM1958
chr7:108,418,960-108,422,359 (-) = 3,400bp @mapq 60 NM0
chr7:108,422,360-108,987,620 (+) = 565,261bp @mapq 60 NM3458

However, when navigating to the region (defined as region in the IGV screenshot shared below), the expected 3,400bp supplementary alignment is not visible in IGV. Any idea of why this can be happening?

Thanks!

[jrobinso]

If it's not shown it's likely either not in the file, or marked "vendor failed". The popup view is created based on the "SA" tag of the alignment you clicked on, this does not guarantee the alignment is in the file, although it would be rare that it is not.

I can't really speculate more without the file.