Column | Description |
|---|---|
ID | System-generated ID for the region. |
Region Name | The region description from Column 4 of the BED file that was used to create the panel. |
Chrom | The chromosome on which the region is located. |
ChromRegionStart | The starting chromosome position for the region. |
ChromRegionEnd | The ending chromosome position for the region. |
Note: Together, the ChromRegionStart and ChromregionEnd make up the chromosome position range. | |
Chrom:Start-End | The chromosome position range appended to the chromosome number. |
% Covered | The percentage of the region that has reads aligned to it. |
Average Coverage | The average coverage (average number of aligned reads) for the region. |
Minimum Coverage | The minimum coverage (number of reads aligned) for any position within the region. |
% Covered Threshold | The percentage of the region that must have reads aligned to it, or the region does not pass the Quality Control settings that have been set for the run’s panel. See To specify the global Quality Control settings. |
Average Coverage Threshold | The average coverage (average number of aligned reads) required for the region, or the region does not pass the Quality Control settings that have been set for the run’s panel. See To specify the global Quality Control settings.. |
Minimum Coverage Threshold | The minimum coverage (number of reads aligned) that is required for any position within the region, or the region does not pass the Quality Control settings that have been set for the run’s panel. See To specify the global Quality Control settings. |
Status | Indicates if the region passed or failed the Quality Control (coverage) settings that were specified for the run’s panel. You can manually change the status for a region. If you manually change the status for a region, then the Update Panel Region dialog box opens. The dialog box lists the new status for the region, and you have the option of adding comments for the status change. The comments are displayed in the Status Comment field. Note: By default, only two statuses, Passed or Failed, are available, and one of these two statuses is always automatically selected for the region. You have the option of adding custom Panel Region statuses and manually selecting a status for a region. See Managing Objects in the Geneticist Assistant Database. |
Average % Covered | Average of the percent covered for the region across all samples for the panel. |
Average Average Coverage | The average of the average coverage values for the region across all samples for the panel. |
Average Minimum Coverage | The average minimum coverage for the region across all samples for the panel. |
Passed | The total number of samples for the panel for which the status of the region is Passed. |
Passed Percent | The percent of the samples for the panel for which the status of the region is Passed. |
Failed | The total number of samples for the panel for which the status of the region is Failed. |
Total | The total number of samples that were submitted for the panel. |
Gene | The gene on which the region is located. |
Transcript | The accession number for the mRNA transcript. |
Protein | The accession number for the protein transcript. |
Exon Number | The coding exon number for the region. |
SD % Covered | The standard deviation for the % Covered value across all samples for the panel. |
SD Average Coverage | The standard deviation for the Average Coverage value across all samples for the panel. |
SD Minimum Coverage | The standard deviation for the Minimum Coverage value across all samples for the panel. |