GenomeLab™ Sequencing Base Calling Quality Values Tables

Introduction:

The GeXP Genetic Analysis Systems produce two estimated error probabilities for each called base. The estimated error probabilities aid users in performing various data analysis tasks, including: quality weighted sequence assembly, sequence trimming for various purposes such as unweighted sequence assembly, primer selection, single-pass (e.g. EST) sequence editing, quality-weighted homology searching, etc. The first estimated error probability is called the Quality Value (QV) and provides an estimate that will discern between various degrees of high-quality bases ("low" error probability) for purposes as quality-weighted sequence assembly and automated primer selection. The second estimated error probability is called the Call Score (CS) and provides an estimate that will discern between various degrees of lower-quality bases ("high" error probability) for purposes such as sequence trimming and single-pass sequence editing.

Both QVs and CSs can be viewed in the Sequence Analysis software module of the GeXP. QVs are exported as part of the PHD file export and as part of the FASTA file export. CSs can only be exported as part of the Text file export.

The download file below contains the updated versions of the Tables that were rebuilt using over 9 million bases.

Instructions:

Download the file qvupdate.exe (642 KB) to a temporary folder (this can also be saved onto a disk for transfer to your GeXP instrument).
Double-click the qvupdate.exe self-extracting file to install the software.
Follow the prompts through the installation process.
To verify that the correct versions of the Quality Value and Call Score Tables were installed check their modified date in the file properties dialog. - Using Windows* Explorer navigate to the d:\ceq8000\bin folder. Right-click on the file name PhredTableFile.qvt and select "Properties" to verify that the modified date is July 31, 2002.
Download A-1940A: Call Scores and Quality Values: Two Measures of Quality Produced by the GeXP Genetic Analysis Systems (PDF Format).

* All trademarks are the property of their respective owners. Where applicable, the PCR process is covered by patents owned by Roche Molecular Systems, Inc., and F. Hoffmann-LaRoche, Ltd.

Additional GeXP Information:

The GenomeLab GeXP Systems are for Laboratory Use Only; not for use in diagnostic procedures.

The GenomeLab SNPstream is for Research Use Only; not for use in diagnostic procedures.