Table 2. Performance of variant calling at germline SNPs.
| # of Positions | TPR | FPR | FNR | |||
| Homozygous Sites | Heterozygous Sites | |||||
| UPN461282 | Average: Unsorted Cells | 17 | 1.00 | 0.00 | 0.00 | 0.00 |
| Average: Single Cells | 9 | 0.90 | 0.00 | 0.00 | 0.21 | |
| Average: Two Cells | 8 | 0.88 | 0.00 | 0.00 | 0.25 | |
| UPN182896 | Average: Unsorted Cells | 329 | 0.99 | 0.00 | 0.00 | 0.00 |
| Average: Single Cells | 189 | 0.93 | 0.01 | 0.00 | 0.13 | |
| Average: Two Cells | 181 | 0.94 | 0.01 | 0.00 | 0.09 | |
| UPN288033 | Average: Unsorted Cells | 327 | 1.00 | 0.01 | 0.00 | 0.00 |
| Average: Single Cells | 195 | 0.92 | 0.02 | 0.00 | 0.13 | |
| Average: Two Cells | 204 | 0.98 | 0.03 | 0.00 | 0.04 | |
True Positive (TP): ≥1 non-reference allele called by Affymetrix array, ≥1 non-reference allele called by sequencing.
True Negative (TN): 0 non-reference alleles called by Affymetrix array, 0 non-reference alleles called by sequencing.
False Positive (FP): 0 non-reference alleles called by Affymetrix array, ≥1 non-reference allele called by sequencing.
False Negative (FN): ≥1 non-reference allele called by Affymetrix array, ≥0 non-reference alleles called by sequencing.
True Positive Rate (TPR): TP/(TP+FN) = sensitivity = power.
False Positive Rate (FPR): FP/(FP+TN) = 1-specificity.
False Negative Rate (FNR): FN/(TP+FN) = 1 - sensitivity = type II error.