Table 3.
Comparison of ME-Scan results to 1,708 presumably fixed AluYb8/9 insertions in the human reference genome
| Individual | Index | Number of ME-Scan negative loci | False Negative rate (%) | Genotypes checked by PCR1 | Checked and Present by PCR2 |
|---|---|---|---|---|---|
| Replication | |||||
| A | ACCAT | 147 | 8.61 | 18 | 4 |
| A | TATTC | 145 | 8.49 | 18 | 4 |
| Pooling | |||||
| A | ACCAT | 400 | 23.4 | 18 | 4 |
| B | TATTC | 420 | 24.6 | 18 | 2 |
| C | GGTTA | 400 | 23.4 | 17 | 5 |
| D | CGCTA | 164 | 9.60 | 17 | 2 |
| D | TTGAT | 134 | 7.85 | 17 | 2 |
| Combined | All | 1003 | 5.85 | 123 | 23 |
1 The number of genotypes compared differs from sample to sample due to occasional uncertain genotype calls (missing data) in the PCR and gel genotyping assays.
2 These genotypes represent actual false negative ME-Scan results (absent according to ME-Scan, present by PCR.)
3 For 100 of the 1,708 loci, ME-Scan did not observe the insertion-present allele in any of the samples tested ("Combined").