Table 1 |.
Comparison of GRCh38-Y and T2T-Y.
| GRCh38-Y | T2T-Y | %Δ | ||
|---|---|---|---|---|
|
| ||||
| Assembly | Total bases | 57,264,655 | 62,460,029 | +9.1 |
| Assigned bases | 57,227,415 | 62,460,029 | +9.1 | |
| Unlocalized bases | 37,240 | 0 | ||
| Num. gaps | 56 | 0 | ||
| Num. N-bases | 30,812,366 | 0 | ||
|
| ||||
| Annotation | Num. genes | 589 | 693 | +17.7 |
| Protein coding | 66 | 106 | +60.6 | |
| Num. additional genes | 6 | 110 | ||
| Protein coding | 1 | 41 | ||
| Num. transcripts | 681 | 883 | +29.7 | |
| Protein coding | 372 | 488 | +31.2 | |
| Num. additional transcripts | 4 | 206 | ||
| Protein coding | 4 | 120 | ||
|
| ||||
| Ampliconic gene copy numbers | BPY2 | 4 (3, 0) | 4 (3, 0) | 0 |
| CDY | 26 (4, 0) | 26 (4, 0) | 0 | |
| DAZ | 4 (4, 0) | 4 (4, 0) | 0 | |
| HSFY | 8 (2, 0) | 8 (2, 0) | 0 | |
| PRY | 8 (2, 0) | 8 (2, 0) | 0 | |
| RBMY | 32 (6, 4) | 34 (6, 4) | +3.3 | |
| TSPY | 25 (7, 0) | 66 (45, 0) | +164.0 | |
| VCY | 2 (2, 0) | 2 (2, 0) | 0 | |
| XKRY | 8 (0, 2) | 8 (0, 2) | 0 | |
|
| ||||
| Haplogroup | Haplogroup | R-L20 (R1b1a2a1a2b1a1) | J-L816 (J1a2b3a1) | |
| Ancestry | European | Ashkenazi Jewish | ||
|
| ||||
| Repetitive bases | SINE | 2,625,350 | 4,385,917 | +67.1 |
| Retroposon | 18,506 | 18,500 | −0.0 | |
| LINE | 6,378,323 | 6,456,888 | +1.2 | |
| LTR | 4,604,368 | 4,613,537 | +0.2 | |
| DNA/Rolling-circle | 2,626,425 | 4,387,030 | +67.0 | |
| Satellite | 1,578,773 | 14,522,636 | +819.9 | |
| Simple repeat | 1,124,311 | 21,568,381 | +1,818.4 | |
| Other | 705,062 | 972,612 | +37.9 | |
|
| ||||
| All repeat classes | 17,501,283 | 53,004,524 | +202.9 | |
| % repetitive (non-N) | 66.3 | 84.9 | +28.1 | |
|
| ||||
| Accessible with short-reads | 13,785,359 | 14,363,623 | +4.2 | |
Annotation statistics for GRCh38-Y are taken from the RefSeq (v110) annotation, and T2T-Y statistics are taken from a lifted and curated combination of RefSeq (v110) and GENCODE (v35) annotations. Num. additional genes/transcripts are those found exclusively in one assembly compared to the other. Ampliconic gene copy numbers are shown as X(Y,Z) where X = total number of annotated genes; Y = protein-coding genes; and Z = transcribed pseudogenes. %Δ is the percent change from GRCh38-Y to T2T-Y. Blank spaces indicate not applicable.