Table 1.
Assembly statistics for the great ape genomes.
| Ape assembly | CHM13_HSAv1e (human) | YRI_HSAv1 (human) | Clint_PTRv1 (chimpanzee) | GSMRT3.2 (gorilla) | Susie_PABv1 (orangutan) |
|---|---|---|---|---|---|
| Estimated deptha | 72 | 116 | 117 | 86.3 | 94.9 |
| Subread length N50 (kbp)b | 16.2 | 13.4 | 17.4 | 18.6 | 16.6 |
| Contig (number) initial/finalc | 1,923/1,916 | 3,645/3,642 | 4,912/5,037 | 15,997 | 5,771/5,813 |
| Assembly size (Gbp) | 2.88 | 2.88 | 2.99 | 3.08 | 3.04 |
| Contig length >3 Mbp, (Gbp) | 2.65 | 2.27 | 2.45 | 2.42 | 2.48 |
| Contig N50 (Mbp) initial/finalc | 29.26 | 6.60 | 12.76/12.42 | 10.02 | 11.27/11.07 |
| Scaffold N50 (Mbp) | 83.02 | ND | 53.1 | ND | 98.47 |
| Longest contig (Mbp)d | 81 | 27 | 80 | 36 | 53 |
| BAC concordance | 97.11% | 97.73% | 99.13% | 96.85% | 96.75% |
| Sequence accuracy (QV) | 36 | 31 | 33-38 | 30-38 | 28-33 |
| Iso-Seq transcripts | 710,974 | ND | 565,691 | 881,801 | 528,145 |
| Contigs in AGP | ND | ND | 685 | 794 | 544 |
| Contigs aligned to GRCh38f [Gbp] | 407 [2.8] | 1,167 [2.8] | 656 [2.8] | 907 [2.8] | 524 [2.8] |
a
Estimated coverage in raw SMRT subreads based on 3.5 Gbp (gorilla) or 3.2 Gbp (all others) estimated genome size.
b
N50 subread lengths of raw input data.
c
Initial contigs/final contigs are the number of contigs before and after resolving chimeras by optical map comparison. These stats do not consider the NCBI minimum contig length filter.
d
Longest contig without gross assembly error.
e
Haploid genome assembly derived from a complete hydatidiform mole.
f
Contigs with less than 95% of sequence aligning to GRCh38, depth-of-coverage greater than two SDs above the mean, or no coverage were excluded.
ND denotes no data.