Concordance plot is shifted

[donkirkby]

I found a couple of concordance plots where I think the concordance isn't properly aligned with the contig.

In the 230505_M01841_0509_000000000-KNL5D run folder's denovo results, 101636A-HCV_S38_genome_concordance.svg has a large yellow insertion between 1.1 and 1.2 that didn't have any blast matches, but that yellow section shows high concordance. The sections under 1.1 and at the 3' end of 1.2 have very low concordance. I wonder if the high concordance region should be right under 1.2.

In the same folder, 101634AMIDI-MidHCV_S35_genome_concordance.svg has a small reversed blast match, 1.1, and it shows very low concordance. Is there a problem with matching reversed sections, or did blast match even on such low concordance?

In the same folder, 101631A-HCV_S28_genome_concordance.svg has the opposite problem: high concordance on a region that hasn't blast matched to anything. What is it concordant with?

In the 230428_M01841_0508_000000000-KNKJP folder, 101627AMIDI-MidHCV_S39_genome_concordance.svg looks like the concordance might be aligned with the reference instead of the contig.