# Metrics Appendix

## Sample Level Metrics

Sample level metrics are found in the sample/row-level metadata in the ADAT.

<table><thead><tr><th width="136">Metric</th><th>ADAT Field</th><th>Applied To</th><th>Threshold</th><th>Impact to Sample</th></tr></thead><tbody><tr><td>Minimum SOMAmer Read Count</td><td>SOMAmerReads; SOMAmerReads_PassFlag</td><td>Non-Blank Samples</td><td>SOMAmerReads > 10 million</td><td>PASS/FLAG</td></tr><tr><td>Maximum SOMAmer Normalized Read Count</td><td>SOMAmerNormReads; SOMAmerNormReads_PassFlag</td><td>Blank Samples</td><td>SOMAmerNormReads &#x3C; 20 million reads</td><td>PASS/FLAG</td></tr><tr><td>Hybridization Normalization</td><td>HybNorm_1_ScaleFactor; HybNorm_PassFlag</td><td>Non-Blank Samples</td><td>0.4 ≤ HybNorm_1_ScaleFactor ≤ 2.5</td><td>PASS/FLAG</td></tr><tr><td>Internal Reference Median Normalization</td><td>MedNormInt_5e-05_ScaleFactor; MedNormInt_0.005_ScaleFactor; MedNormInt_0.2_ScaleFactor; MedNormInt_PassFlag</td><td>Individual Blank and Calibrator samples, split by dilution group</td><td>0.4 ≤ MedNormInt_5e-05_ScaleFactor ≤ 2.5<br><br>0.4 ≤ MedNormInt_0.005_ScaleFactor ≤ 2.5<br><br>0.4 ≤ MedNormInt_0.2_ScaleFactor ≤ 2.5</td><td>PASS/FLAG</td></tr><tr><td>External Reference Median Normalization</td><td>MedNormExt_5e-05_ScaleFactor; MedNormExt_0.005_ScaleFactor; MedNormExt_0.2_ScaleFactor; MedNormExt_PassFlag</td><td>Individual non-control and QC samples, split by dilution group</td><td>0.4 ≤ MedNormExt_5e-05_ScaleFactor ≤ 2.5<br><br>0.4 ≤ MedNormExt_0.005_ScaleFactor ≤ 2.5<br><br>0.4 ≤ MedNormExt_0.2_ScaleFactor ≤ 2.5<br><br></td><td>PASS/FLAG</td></tr><tr><td>TM Controls</td><td>EmpiricalHybTemp; EmpiricalHybTemp_PassFlag</td><td>All samples</td><td>EmpiricalHybTemp &#x3C; 52.4</td><td>PASS/FLAG</td></tr><tr><td>Row Check</td><td>RowCheck_PassFlag</td><td>All samples</td><td>PLATE_FAIL if the sample is on a plate that received a FAIL. Otherwise, PASS if all Pass Flags in this row are PASS and FLAG if not.</td><td>PASS/FLAG/PLATE_FAIL</td></tr></tbody></table>

## SOMAmer Level Metrics

SOMAmer level metrics are found in the SOMAmer/column-level metadata in the ADAT.

<table><thead><tr><th width="290.765625">Metric</th><th>ADAT Field</th></tr></thead><tbody><tr><td>Platform Specific Calibration</td><td>PlatformSpecificCalibrate_&#x3C;PlateBarcode>_ScaleFactor</td></tr><tr><td>Cross Platform Calibration</td><td>CrossPlatformCalibrate_&#x3C;PlateBarcode>_ScaleFactor</td></tr><tr><td>QC Check</td><td>QCCheck_&#x3C;PlateBarcode>_ScaleFactor</td></tr></tbody></table>

## Plate Level Metrics

Plate level metrics are found in the header metadata in the ADAT.

| Metric                        | ADAT Field                                                                           | Threshold                                          | Impact to Plate |
| ----------------------------- | ------------------------------------------------------------------------------------ | -------------------------------------------------- | --------------- |
| QC Percent in Tails           | QCCheckTailPercent; QCCheckTailPercent\_PassFlag                                     | QCCheckTailPercent < 15%                           | PASS/FAIL       |
| Calibration Percent in Tails  | PlatformSpecificCalibrateTailPercent; PlatformSpecificCalibrateTailPercent\_PassFlag | PlatformSpecificCalibrateTailPercent < 15%         | PASS/WARNING    |
| SOMAmer Normalized Reads      | PlateSOMAmerNormReads\_PassFlag                                                      | < 70% of blank samples flagged at SOMAmerNormReads | PASS/WARNING    |
| Platform Specific Plate Scale | PlatformSpecificPlateScale\_ScaleFactor                                              | N/A                                                | N/A             |
| Cross Platform Plate Scale    | CrossPlatformPlateScale\_ScaleFactor                                                 | N/A                                                | N/A             |
| Cross Platform Calibration    | CrossPlatformCalibrationTailPercent                                                  | N/A                                                | N/A             |


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