Table 7 Percentage of truly somatic (S) and germline (G) insertions, among the insertions predicted in the TD but not the ND sample, eliminated according to various cutoff values. The cutoff corresponds to the percentage of discordant reads in a 400bp window around the TEI and is used to determine the presence of a FN in the ND sample
From: Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
% predictions eliminated | ||||||
|---|---|---|---|---|---|---|
10X | 20X | 40X | ||||
Discordant read cutoff | S | G | S | G | S | G |
> 1% | 0.00 | 97.73 | 6.15 | 98.17 | 1.54 | 100.00 |
> 1.5% | 0.00 | 95.45 | 4.62 | 95.41 | 0.00 | 100.00 |
> 2% | 0.00 | 90.91 | 0.00 | 94.50 | 0.00 | 100.00 |
> 2.5% | 0.00 | 83.33 | 0.00 | 86.24 | 0.00 | 100.00 |
> 3% | 0.00 | 79.55 | 0.00 | 81.65 | 0.00 | 93.94 |