Dual-indexed library: String of G's for 1 of the 2 Indexes - Adapter Dimers?

[7891_ZA]

A dual-indexed library was sequenced on the Illumina iSeq100.

When looking at the most popular index pairs within the DemultiplexSummaryF1L1.txt file, there seems to reads where only one of the two Indexes are detected, while the other is represented by a string of G's.

As I understand, those reads that display a string of G's for both the Index 1 and Index 2 most likely represent the non-indexed PhiX.

But what about the case for those reads that have a string of G's for only one of the two Indexes? Could this be related to adapter dimers?

What would one expect in the DemultiplexSummaryF1L1.txt file for adapter dimers, as they would be able to cluster..

[GenoMax]

If possible have Illumina tech support have a look at this run. Something could be wrong with it. Poly-G generally means there was no signal for 1- and 2-color runs. It is theoretically possible that the sample was over-clustered and sequencer had trouble basecalling/sequencing index 2.

[nucacidhunter]

It is most likely sequencing cartridge related. If you have images of cycles, you can compare index 2 cycle images with index 1 images.

Illumina would replace sequencing kit.