Run Indexing QC

What is it

The Indexing QC page lists count information for indexes used in the run as designated in the sample sheet. The Indexing QC is only available if the run is an index run.

When to use it

Look at this page when you want to see indexing information for a lane after the index read is completed.

When not to use it

This page only provides indexing information. Do not use it for runs that were not indexed, or to look at other primary, secondary, or tertiary analysis metrics. This information is a quick estimation and can vary slightly from final output.

How to use it

You can select the displayed lane through the drop-down list. The first table provides an overall summary of the indexing performance for that lane, including:

Total Reads The total number of reads for this lane
PF Reads The total number of passing filter reads for this lane
% Reads Identified (PF) The total fraction of passing filter reads assigned to an index
CV The coefficient of variation for the number of counts across all indexes
Min The lowest representation for any index
Max The highest representation for any index

Further information is provided regarding the frequency of individual indexes in both table and graph form. The table contains several columns, including

Index Number A unique number assigned to each index by BaseSpace Sequence Hub for display purposes
Sample ID The sample ID assigned to an index in the sample sheet
Project The project assigned to an index in the sample sheet
Index 1 (I7) The sequence for the first index read
Index 2 (I5) The sequence for the second index read
% Reads Identified (PF) The number of reads (only includes Passing Filter reads) mapped to this index

This information is also displayed in graphical form. In the graphical display, indexes are ordered according to the unique Index Number assigned by BaseSpace Sequence Hub.

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