Metrics Appendix

Sample Level Metrics

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

Metric	ADAT Field	Applied To	Threshold	Impact to Sample
Minimum SOMAmer Read Count	SOMAmerReads; SOMAmerReads_PassFlag	Non-Blank Samples	SOMAmerReads > 10 million	PASS/FLAG
Maximum SOMAmer Normalized Read Count	SOMAmerNormReads; SOMAmerNormReads_PassFlag	Blank Samples	SOMAmerNormReads < 40 million reads	PASS/FLAG
Hybridization Normalization	HybNorm_1_ScaleFactor; HybNorm_PassFlag	Non-Blank Samples	0.4 ≤ HybNorm_1_ScaleFactor ≤ 2.5	PASS/FLAG
Internal Reference Median Normalization	MedNormInt_5e-05_ScaleFactor; MedNormInt_0.005_ScaleFactor; MedNormInt_0.2_ScaleFactor; MedNormInt_PassFlag	Individual Blank and Calibrator samples, split by dilution group	0.4 ≤ MedNormInt_5e-05_ScaleFactor ≤ 2.5 0.4 ≤ MedNormInt_0.005_ScaleFactor ≤ 2.5 0.4 ≤ MedNormInt_0.2_ScaleFactor ≤ 2.5	PASS/FLAG
External Reference Median Normalization	MedNormExt_5e-05_ScaleFactor; MedNormExt_0.005_ScaleFactor; MedNormExt_0.2_ScaleFactor; MedNormExt_PassFlag	Individual non-control and QC samples, split by dilution group	0.4 ≤ MedNormExt_5e-05_ScaleFactor ≤ 2.5 0.4 ≤ MedNormExt_0.005_ScaleFactor ≤ 2.5 0.4 ≤ MedNormExt_0.2_ScaleFactor ≤ 2.5	PASS/FLAG
Correlation with Reference	RefCorr; RefCorr_PassFlag	Blank Samples	RefCorr < 0.6	PASS/FLAG
TM Controls	EmpiricalHybTemp	All samples	N/A	N/A
Row Check	RowCheck_PassFlag	All samples	The row check shall be PASS is all Pass Flags in this row are PASS; otherwise it shall be FLAG	PASS/FLAG

SOMAmer Level Metrics

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

These PASS/FAIL designations are only used for plate level quality control. They should not be used to assess SOMAmer quality.

Metric	ADAT Field	Threshold	Impact to SOMAmer
Platform Specific Calibration	PlatformSpecificCalibrate_<PlateBarcode>_ScaleFactor; PlatformSpecificCalibrate_<PlateBarcode>_PassFlag	0.6 < PlatformSpecificCalibrate_<PlateBarcode>_ScaleFactor < 1.4	PASS/FAIL
Cross Platform Calibration	CrossPlatformCalibrate_<PlateBarcode>ScaleFactor; CrossPlatformCalibrate<PlateBarcode>_PassFlag	0.6 < PCrossPlatformCalibrate_<PlateBarcode>_ScaleFactor < 1.4	PASS/FAIL
QC Check	QCCheck_<PlateBarcode>ScaleFactor; QCCheck_<PlateBarcode>_PassFlag	0.8 < QCCheck_<PlateBarcode>ScaleFactor < 1.2	PASS/FAIL

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
Reference Correlation	PlateRefCorr_PassFlag	< 70% of blank samples flagged at RefCorr	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