Table 1.
Summary of 15 assembled TCAF haplotypes constructed using large-insert BAC libraries and long-read sequencing.
| Haplotype ID | BAC library (species or population) | Length (bp) | Length of TCAF SD cassettes (bp) | Copy number of TCAF SD cassettes | % GC | Haplogroup |
|---|---|---|---|---|---|---|
| CHM1 | CHM1 | 368,013 | 277,806 | 2 | 39.83 | Haplogroup 2-1 |
| VMRC53_hapA | NA12878 (European) | 433,048 | 277,806 | 2 | 39.56 | Haplogroup 2-2 |
| VMRC53_hapB | NA12878 (European) | 425,306 | 273,483 | 2 | 39.63 | Haplogroup 3-2 |
| VMRC61_hapA | HG00732 (Puerto Rican) | 337,690 | 277,856 | 2 | 39.91 | Haplogroup 2-2 |
| VMRC61_hapB | HG00732 (Puerto Rican) | 435,583 | 405,366 | 3 | 39.71 | Haplogroup 4 |
| VMRC62_hapA | HG00733 (Puerto Rican) | 395,405 | 277,854 | 2 | 39.60 | Haplogroup 2-2 |
| VMRC64_hapA | NA19240 (Yoruba) | 323,367 | 260,853 | 2 | 39.94 | Haplogroup 2-2 |
| VMRC64_hapB | NA19240 (Yoruba) | 348,654 | 277,808 | 2 | 40.07 | Haplogroup 2-2 |
| VMRC66_hapA | NA19434 (Luhya) | 496,357 | 406,131 | 3 | 40.00 | Haplogroup 5 |
| VMRC69_hapA | HG00514 (Han Chinese) | 387,079 | 277,712 | 2 | 39.29 | Haplogroup 3-1 |
| VMRC73_hapA | GM10539 (Melanesian) | 247,628 | 145,427 | 1 | 39.93 | Haplogroup 1 |
| VMRC73_hapB | GM10539 (Melanesian) | 222,558 | 145,424 | 1 | 39.85 | Haplogroup 1 |
| CH251_contig | CH251 (Pan troglodytes) | 273,442 | 127,988 | 1 | 39.90 | Ancestral-like |
| CH277_contig | CH277 (Gorilla gorilla) | 241,956 | 140,234 | 1 | 39.98 | Ancestral-like |
| CH250_contig | CH250 (Rhesus macaque) | 225,909 | 140,184 | 1 | 40.49 | Ancestral-like |
BAC clones were selected and sequenced using the PacBio long-read sequencing technology and assembled into individual haplotypes (Methods). Copy number of TCAF segmental duplication (SD) cassettes and the classification for individual haplotypes were determined by Miropeats and sequence alignment analysis (Fig. 2 and Supplementary Figs. 5–13).