TE library | Reference TPa | Reference FNb | NA12878 TPc | NA12878 FNd | FPe | Validated Novelf |
|---|
L1HS | 589 (84642) | 35 | 54 (1493) | 22 | 19 (74) | 10 (38) |
AluYa5/8 | 2335 (51529) | 404 | 143 (874) | 91 | 9 (44) | 6 (32) |
AluYb8/9 | 1664 (61099) | 183 | 119 (953) | 29 | 3 (12) | 1 (4) |
- aReference TP, observed TE insertions (reads) in the reference truth set with a TE cluster within 600 bp window of 3′ terminal position and match to predicted TE subfamily. Clusters contain filtered reads with a minimum 2 or more Illumina read 1 derived from the unique flanking sequence. See text for details
- bReference FN, false negatives computed as reference TE subfamily members lacking cluster within 600 bp window of TE 3′ terminal position
- cNA12878 TP, observed 1000 Genomes Phase 3 MEI calls in NA12878 having an identified TE cluster within 600 bp window of 3′ terminal position and matching predicted TE class (Alu, LINE1)
- dNA12878 FN, MEI calls with TE subfamily classification lacking an observed cluster within 600 bp window of TE 3′ terminal position
- eFP, false positive clusters lacking previous evidence of TE insertion within 600Â bp window of cluster position before validation with GiaB and ONT long-read data
- fValidated Novel, FP clusters supported by evidence from GiaB and ONT long-read data
