Table 1.
Details of cross-validation between Gauchian and ONT.
| Samplea | CN change | Other variants | CNV | Variant type | Number of samples |
|---|---|---|---|---|---|
| NA20756 | 1 | Gain | CNG with no other variant | 11 | |
| HG01912 | 3 | ||||
| HG01889 | 5 | ||||
| HG02284 | 6 | ||||
| HG03547 | 3 | ||||
| NA19909 | 4 | ||||
| HG03895 | 1 | ||||
| NA18917 | 2 | ||||
| NA19711 | 2 | ||||
| HG03575 | 4 | ||||
| Brain-S1 | 1 | ||||
| PP-3307* | 1 | p.L483P | CNG + SNV | 1 | |
| Brain-S2 | 4 | c.1263del+RecTL | CNG + c.1263del+RecTL conversion | 2 | |
| Brain-S3 | 4 | c.1263del+RecTL | |||
| HG03428 | −1 | Loss | CNL, non-pathogenic | 3 | |
| NA19024 | −1 | ||||
| PP-12224 | −1 | ||||
| HG00422 | −1 | RecNciI | Pathogenic CNL (RecNciI CNL) | 1 | |
| Brain-S4 | −1 | p.L483P | Non-pathogenic CNL + p.L483P | 1 | |
| HG00119 | 0 | c.1263del+RecTL | No CN change | Gene conversion | 2 |
| HG00115 | 0 | c.1263del+RecTL | |||
| PP-3420 | 0 | p.L483P | SNV | 9 | |
| PP-3700 | 0 | p.L483P | |||
| PP-57787 | 0 | p.L483P | |||
| PP-59343 | 0 | p.L483P | |||
| PP-59926 | 0 | p.L483P | |||
| PP-60060 | 0 | p.L483P | |||
| Brain-S5 | 0 | p.L483P | |||
| PP-41342* | 0 | p.L483P/p.E365K | |||
| PP-3429 | 0 | p.A495P | |||
| PP-3762*,PP-42378*,PP-3476,PP-3179,PP-3001,PP-3173,PP-3023,PP-42444,PP-3406,PP-56534,PP-52772,PP-41705 | 0 | No GBA variants | 12 | ||
Samples with * were discordant with BWA-GATK.
aSamples with IDs starting with NA- and HG- were obtained from NHGRI; samples with IDs starting with PP were obtained from PPMI; samples marked as brain were obtained from QSBB.