Table 1.
Assembly metrics for the six libraries we built from NA12878 and NA24385 (L1–L6) and a previously published 10X Genomics library (L7); data was downsampled for Supernova to its acceptable maximum of ca. 60× by its parameter “--maxreads”.
| Raw coverage C (X) | CF (X) | CR (X) | Contig N50 (bp) | Contig NA50 (bp) | Diploid fraction (%) | Genome fraction (%) | |
|---|---|---|---|---|---|---|---|
| NA12878 | |||||||
| L1_Aquila | 103 | 123 | 0.41 | 34,759 | 31,645 | 98.1 | 95.45 |
| L1_Supernova | 58,408 | 57,254 | 73.3 | 93.69 | |||
| L2_Aquila | 192 | 334 | 0.27 | 94,699 | 91,662 | 96.7 | 94.43 |
| L2_Supernova | 144,298 | 136,253 | 58.9 | 94.81 | |||
| L3_Aquila | 106 | 958 | 0.07 | 120,963 | 116,438 | 98.7 | 96.17 |
| L3_Supernova | 114,900 | 111,388 | 77.2 | 94.62 | |||
| L7_Aquila | 78 | 243 | 0.32 | 78,309 | 75,378 | 97.1 | 95.32 |
| NA24385 | |||||||
| L4_Aquila | 100 | 208 | 0.25 | 96,558 | 93,132 | 98.2 | 96.98 |
| L4_Supernova | 99,516 | 96,510 | 79.2 | 95.01 | |||
| L5_Aquila | 100 | 803 | 0.08 | 135,115 | 130,176 | 98.8 | 96.77 |
| L5_Supernova | 129,195 | 125,339 | 78.1 | 94.86 | |||
| L6_Aquila | 100 | 1504 | 0.05 | 125,064 | 120,490 | 98.7 | 96.62 |
| L6_Supernova | 101,236 | 98,364 | 73.4 | 94.69 | |||
| L5+L6_Aquila | 200 | 2307 | 0.07 | 177,974 | 172,358 | 99.1 | 97.06 |
CF physical (‘fragment’) coverage; CR read coverage; C raw coverage ≥ CF × CR. Genome fraction, percentage of reference genome that is covered by the assembly. Diploid fraction, percentage of genome fraction that is covered by exactly two parental contigs. L5 + L6 describes performance for a simple combination of the data from libraries 5 and 6. The statistics of the female individual, NA12878, include the X chromosome; those of the male individual, NA23485, include the X chromosome but not the Y chromosome.