Table 1.
Comparison of GRCh38 and T2T-CHM13v1.1 human genome assemblies.
| Summary | GRCh38 | T2T-CHM13 | ±% |
|---|---|---|---|
| Assembled bases (Gbp) | 2.92 | 3.05 | +4.5% |
| Unplaced bases (Mbp) | 11.42 | 0 | −100.0% |
| Gap bases (Mbp) | 120.31 | 0 | −100.0% |
| # Contigs | 949 | 24 | −97.5% |
| Ctg NG50 (Mbp) | 56.41 | 154.26 | +173.5% |
| # Issues | 230 | 46 | −80.0% |
| Issues (Mbp) | 230.43 | 8.18 | −96.5% |
|
| |||
| Gene Annotation | |||
|
| |||
| # Genes | 60,090 | 63,494 | +5.7% |
| protein coding | 19,890 | 19,969 | +0.4% |
| # Exclusive genes | 263 | 3,604 | |
| protein coding | 63 | 140 | |
| # Transcripts | 228,597 | 233,615 | +2.2% |
| protein coding | 84,277 | 86,245 | +2.3% |
| # Exclusive transcripts | 1,708 | 6,693 | |
| protein coding | 829 | 2,780 | |
|
| |||
| Segmental duplications (SDs) | |||
|
| |||
| % SDs | 5.00% | 6.61% | |
| SD bases (Mbp) | 151.71 | 201.93 | +33.1% |
| # SDs | 24097 | 41528 | +72.3% |
|
| |||
| RepeatMasker | |||
|
| |||
| % Repeats | 51.89% | 53.94% | |
| Repeat bases (Mbp) | 1,516.37 | 1,647.81 | +8.7% |
| LINE | 626.33 | 631.64 | +0.8% |
| SINE | 386.48 | 390.27 | +1.0% |
| LTR | 267.52 | 269.91 | +0.9% |
| Satellite | 76.51 | 150.42 | +96.6% |
| DNA | 108.53 | 109.35 | +0.8% |
| Simple repeat | 36.5 | 77.69 | +112.9% |
| Low complexity | 6.16 | 6.44 | +4.6% |
| Retroposon | 4.51 | 4.65 | +3.3% |
| rRNA | 0.21 | 1.71 | +730.4% |
GRCh38 summary statistics exclude “alts” (110 Mbp), patches (63 Mbp), and Chromosome Y (58 Mbp). Assembled bases: all non-N bases. Unplaced bases: not assigned or positioned within a chromosome. # Contigs: GRCh38 scaffolds were split at three consecutive Ns to obtain contigs. NG50: half of the 3.05 Gbp human genome size contained in contigs of this length or greater. # Exclusive genes/transcripts: for GRCh38, GENCODE genes/transcripts not found in CHM13; for CHM13, extra putative paralogs that are not in GENCODE. Segmental duplication analysis is from (42). RepeatMasker analysis is from (49).