Table 1.
Demographics, and sequencing and assembly metrics for the cohort
| Sex | Male | 63 (66%) | ||
| Female | 33 (34%) | |||
| Predicted major genetic ancestry | European (EUR) | 71.88% | ||
| African (AFR) | 20.83% | |||
| Admixed American (AMR) | 3.13% | |||
| Southeast Asian (SAS) | 1.04% | |||
| Unspecified Admixed (UNKNOWN) | 3.13% | |||
| Median | Min | Max | ||
| Sequencing metrics | Sequenced bases (Gb) | 80.9 | 53.5 | 131.5 |
| Mean read length (sequenced) | 16,771 | 11,295 | 21,412 | |
| Median coverage (X) | 27 | 18 | 44 | |
| Percent covered at 10x | 97.80% | 95.10% | 99.00% | |
| Percent covered at 20x | 84.90% | 36.10% | 97.50% | |
| Proband assembly N50 (Mb) | All contigs | 29.05 | 2.10 | 71.30 |
| Maternal contigs | 29.30 | 2.10 | 71.30 | |
| Paternal contigs | 28.70 | 2.20 | 67.90 | |
| hap1 contigs | 31.70 | 18.20 | 42.90 | |
| hap2 contigs | 27.85 | 14.40 | 40.80 | |
| Small variant metrics (DeepVariant) | SNVs | 4,404,564 | 3,997,350 | 5,299,670 |
| Total indels | 970,031 | 926,286 | 1,153,616 | |
| Structural variant metrics (pbsv) | Total structural variants | 55,586 | 53,834 | 65,120 |
| Deletion | 24,757 | 23,799 | 29,531 | |
| Duplication | 3017 | 2820 | 3649 | |
| Insertion | 27,594 | 26,441 | 32,437 | |
| Inversion | 121 | 99 | 155 | |
| Breakend | 193 | 124 | 312 | |
| Structural variants >50 bp | 25,218 | 23,994 | 29,159 | |
| Deletion | 10,303 | 9804 | 12,306 | |
| Duplication | 641 | 536 | 742 | |
| Insertion | 14,012 | 13,344 | 16,159 | |
| Inversion | 121 | 99 | 155 | |
| Breakend | 193 | 124 | 312 |
