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Table 3 Comparison of ME-Scan results to 1,708 presumably fixed AluYb8/9 insertions in the human reference genome

From: Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

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. 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. 2 These genotypes represent actual false negative ME-Scan results (absent according to ME-Scan, present by PCR.)
  3. 3 For 100 of the 1,708 loci, ME-Scan did not observe the insertion-present allele in any of the samples tested ("Combined").