Table 1.
Data quality of the three sequencing runs.
| Chip ID | Sample number | Final reads | TF alignment | Reads passed length filteringa | Barcode and primer sortingb | Downstream barcode identificationc | Matched reads | Reads of each sample (mean ± std.dev) | Reads of per locus per sample(mean ± std.dev) | Reads of per locus per sample | Sample% reported more than 15 loci |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 150 | 4.4 M | 95% | 4.27 M | 4.0 M | 3.7 M | 3.6 M | 24,053 ± 24,318 | 1,503 ± 1,520 | 352~4,466 | 94% |
| 2 | 151 | 4.4 M | 97% | 4.24 M | 4.1 M | 3.7 M | 3.7 M | 24,244 ± 26,667 | 1,515 ± 1,667 | 381~4,018 | 95% |
| 3 | 150 | 4.3 M | 96% | 4.08 M | 3.9 M | 2.5 M | 2.4 M | 15,712 ± 14,271 | 982 ± 892 | 183~2,311 | 97% |
| 4 | 150 | 3.6 M | 94% | 3.47 M | 3.2 M | 2.9 M | 2.9 M | 19,273 ± 18,228 | 1,205 ± 1,139 | 283~3,214 | 93% |
| Average | 150 | 4.2 M | 95.5% | 4.02 M | 3.8 M | 3.2 M | 3.1 M | 20,826 ± 21,689 | 1,301 ± 1,355 | 359~3,503 | 94.8% |
aLength filtering was performed by giving up the reads less than 60 bp.
bBarcode and primer sorting was processed by perfect matching to barcode (10 bp) and forward primer sequences (19–23 bp).
cDownstream barcodes were specifically chosen sequences (5–10 bp) downstream of the short tandem repeat (STR) repeat region. Detection of this downstream barcode may help to obtain reads that cover the entire STR repeat region. Perfect matching was applied in this filtering step.