Table 2. Systematic comparison of assembly quality.
| Assembly | Total sequence length (bp) | Scaffold or contig N50 (Mb)/L50 | GRCh38 recovery rate (%) | Segmental duplication length (bp) | Repeat length (bp) | Detected RefSeq genes (intact only) |
|---|---|---|---|---|---|---|
| GRCh38C | 3,209,286,105 | 67.79/16 | — | 212,777,868 (6.63%) | 1,564,209,365 (48.74%) | 20,135 |
| KOREF_CS,L,M | 3,211,075,818 | 26.46/35 | 88.47 (scaffolds) | 149,353,191 (4.65%) | 1,452,404,484 (45.23%) | 17,758 |
| CHM1_PacBio_r2L | 2,996,426,293 | 26.90/30 | 88.02 | 205,559,250 (6.86%) | 1,541,211,387 (51.43%) | 17,657 |
| CHM1_1.1S,B | 3,037,866,619 | 50.36/20 | — | 157,426,845 (5.18%) | 1,417,977,130 (46.68%) | 18,040 |
| NA12878_singleL,M | 3,176,574,379 | 26.83/37 | 88.26 | 168,652,649 (5.31%) | 1,545,168,387 (48.64%) | 6,610 |
| NA12878_AllpathsS | 2,786,258,565 | 12.08/67 | 82.89 | 90,343,965 (3.24%) | 1,250,655,296 (44.89%) | 16,995 |
| HuRefC | 2,844,000,504 | 17.66/48 | 85.85 | 134,317,812 (4.72%) | 1,411,487,301 (49.63%) | 16,968 |
| MongolianS | 2,881,945,563 | 7.63/111 | 86.54 | 121,384,034 (4.21%) | 1,399,420,366 (48.56%) | 17,189 |
| YH_2.0S | 2,911,235,363 | 20.52/39 | 86.31 | 127,254,909 (4.37%) | 1,397,013,571 (47.99%) | 17,125 |
| AfricanS | 2,676,008,911 | 0.062/11,689 | 69.47 | 55,830,170 (2.09%) | 968,988,149 (36.21%) | 9,167 |
NGS, next-generation sequencing. Major sequencing and mapping data used in the assembly are marked by superscript letters: C, chain-terminating Sanger sequences; B, indexed BAC end sequences; L, long reads; M, genome maps; S, NGS short reads.