Calculated library statistics

As you create, view, edit, or review a library, these statistics can appear.

Statistic	Description
% Occupied before auto replication	The fraction of the total features in the library that are occupied by the requested number of baits, including any Agilent quality control baits. However, eArray automatically includes as many complete sets of baits as will fit in the available space in the library. These additional "auto replicated" sets of baits are not included in the calculation of this value. Example: Your library contains 12,000 baits, including the required Agilent control baits. The capacity of the 1 X 55K library format is 57,750 baits. Thus, the value of % Occupied before auto replication is 12,000 baits / 57,750 baits = 20.7792%. However, because of auto replication, eArray actually includes a total of four complete sets of baits in your library (12,000 x 4 = 48,000 baits). Five complete sets would exceed the capacity of the library format (12,000 x 5 = 60,000 baits). Additional auto replicated sets of baits are not included in the calculation of % Occupied before auto replication.
Number of Available Features	The number of unassigned features remaining in the library. You can use these unassigned features to accommodate additional baits, or to increase the replicate count of selected bait groups in the library. Example: You design a library that contains 12,000 baits, including all requested replicates, and the Agilent control bait group. The currently available library format (1 X 55K) accommodates a maximum of 57,750 baits. Thus, Number of Available Features = 57,750 - 12,000 = 45,750. (SureSelect Target Enrichment application type only) For library sets, this value reflects the number of features that are available collectively in all libraries in the library set.
Number of Libraries	For the SureSelect RNA Enrichment application type, which supports only single custom libraries that each contain up to 57,750 baits, this value is always 1. For the SureSelect Target Enrichment application type, this value is 1 for single custom libraries. If you design a library that exceeds the capacity of a single library, eArray automatically creates a library set, which distributes the baits over multiple libraries. For library sets, the Number of Libraries value is the total number of libraries in the library set.
Base Coverage	If all baits in the library have chromosomal locations defined for them, this statistic is the total number of bases (in Mb) in the genome of interest (or the corresponding transcripts, as appropriate) that are covered by at least one bait in the library. If one or more baits in the library do not have chromosomal locations defined for them, this statistic is an estimate of the number of bases (in Mb) in the genome of interest (or the corresponding transcripts, as appropriate) that are covered by at least one bait in the library. The estimate is based on the number of unique baits in the library, the bait length, and the bait tiling density. Unless otherwise warranted, eArray assumes a bait tiling density of 2x. If Calculating appears instead of a numerical value, eArray has not yet completed the base coverage calculation. The numerical value appears when it becomes available. If Not Calculated appears instead of a numerical value, eArray has not calculated the base coverage. To calculate this value, click Calculate. If you add or remove baits from a library, or Agilent re-annotates the baits in a library, the base coverage can change. However, eArray does not automatically recalculate base coverage. If an action has been taken that may have changed base coverage, eArray displays the existing base coverage value in red, and a Recalculate button appears next to the value. To recalculate the base coverage based on the current bait content of the library, click Recalculate. The calculation can take some time. When eArray calculates base coverage, it also calculates the number of unique baits (see the next item).
Number of Unique Baits	The number of distinct bait sequences that are represented in the library. If Calculating appears instead of a numerical value, eArray has not yet completed the unique baits calculation. The numerical value appears when it becomes available. If Not Calculated appears instead of a numerical value, eArray has not calculated the number of unique baits. To calculate this value, click Calculate in Base Coverage. If you add or remove baits from a library, or Agilent re-annotates the baits in a library, the number of unique baits can change. However, eArray does not automatically recalculate this value. If an action has been taken that may have changed the number of unique baits, eArray displays the existing unique baits value in red. To recalculate the number of unique baits based on the current bait content of the library, click Recalculate next to the Base Coverage value. The calculation can take some time. eArray calculates the number of unique baits and the base coverage value at the same time (see the previous item).
GC Percent	The percentage of the bases in all baits that are G and C bases.
Agilent Recommended Boosting	The bait boosting that has been applied to the library, if any. One of these values appears: none – No bait boosting has been applied to the library. (When the library was created, edited, or reviewed, the option Maximize capacity was selected in Agilent Recommended Boosting, or the library was created in a previous version of eArray that did not support bait boosting.) all – Bait boosting has been applied to both the catalog and custom baits in the library. (When the library was created, edited, or reviewed, the option Maximize performance was selected in Agilent Recommended Boosting.) For more information about bait boosting, see SureSelect Target Enrichment Libraries.