View Run Indexing QC

Available only for indexed runs, the Indexing QC page provides indexing QC results for the run. View unexpected results for a sample, or confirm that all indexed samples are properly represented.

The first section contains a table that summarizes the indexing performance for the selected lane.

• Total Reads: Total number of reads.

• PF Reads: Total number of clusters passing filter.

• % Reads Identified (PF): Percentage of clusters passing filter that are assigned to an index.

• % Reads Undetermined: Percentage of clusters passing filter that could not be assigned to an index.

• CV: Coefficient of variation for the number of counts across all indexes.

• Min: Lowest representation for any index.

• Max: Highest representation for any index.

The graph displays the % Reads Identified (PF) Per Index for the selected lane.

The second section shows % Reads Identified (PF) Per Index in the Per Index table.

• Index: A unique number BaseSpace Sequence Hub assigns to each index for display purposes.

• Sample ID: The sample ID assigned to an index in the sample sheet.

• Library Name: The library 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): Percentage of clusters passing filter that are assigned to the index.