Illumina summary spreadsheet. What statistics for 4 reads mean

Question

[semion.leyn]

Dear community,

I have a general question, but I can't find answer for it. In the run summary from HiSeq 4000 150x2 run we have sections "Cycle status", "Run Summary", "Read 1", "Read 2", "Read 3", "Read 4". What do these Read 1-4 mean?

Thanks!

Answer 1

[GenoMax]

Read 1 - Read 1/Forward reads
Read 2 - Index 1
Read 3 - Index 2 (dual indexed sample)
Read 4 - Read 2/Reverse reads

In Illumina sequencing, index reads are not part of the main sequencing. Cycle numbers you see in the summary report should indicate above structure.

[semion.leyn]

Thank you very much for such a quick answer!