Indexes Tab
The Indexes tab is only available when a sample sheet is uploaded to the control software during run setup. You also must conduct an index run.
On all systems except MiSeq, this tab is populated when SAV connects to the InterOp folder after running bcl2fastq2 software. Otherwise, this tab is not populated. If the run is connected to BaseSpace Sequence Hub, the indexing information is available there.
Use the Lane drop-down list to select a lane and view the indexing information. The option for all lanes aggregates indexing information from any samples with the same index sequence and sample ID.
The following metrics are provided at the top of the page.
|
Metric |
Description |
|---|---|
|
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. |
The table provides information on the frequency of individual indexes. This information is also displayed in graph format. In the graphs, indexes are ordered by the unique index number SAV assigned.
|
Column |
Description |
|---|---|
|
Index Number |
A unique number assigned to each index by SAV 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. |
