Table 5.
Gene annotation summary.
| Gene category | Gene Biotype | CHM13 | KSA001 | Count of unmapped |
|---|---|---|---|---|
| Protein-coding | protein coding | 19,969 | 19,968 | 1 |
| Non-coding RNA | lncRNA | 17,482 | 17,482 | 0 |
| miRNA | 2,045 | 2,223 | 20 | |
| misc RNA | 2,224 | 2,221 | 3 | |
| Mt rRNA | 3 | 3 | 0 | |
| Mt tRNA | 29 | 29 | 0 | |
| ribozyme | 8 | 8 | 0 | |
| rRNA | 1,007 | 1,007 | 0 | |
| rRNA pseudogene | 506 | 503 | 3 | |
| scaRNA | 48 | 48 | 0 | |
| scRNA | 2 | 2 | 0 | |
| snoRNA | 945 | 944 | 1 | |
| snRNA | 1,886 | 1,883 | 3 | |
| sRNA | 5 | 5 | 0 | |
| TEC | 1,341 | 1,341 | 0 | |
| vault RNA | 1 | 1 | 0 | |
| Pseudogenes | pseudogene | 18 | 15 | 3 |
| polymorphic pseudogene | 50 | 50 | 0 | |
| processed pseudogene | 10,769 | 10,764 | 5 | |
| transcribed processed pseudogene | 551 | 550 | 1 | |
| transcribed unitary pseudogene | 138 | 137 | 1 | |
| transcribed unprocessed pseudogene | 941 | 941 | 0 | |
| translated processed pseudogene | 2 | 2 | 0 | |
| translated unprocessed pseudogene | 1 | 1 | 0 | |
| unitary pseudogene | 98 | 98 | 0 | |
| unprocessed pseudogene | 2,725 | 2,723 | 2 | |
| Immunoglobulin/T-cell receptor | IG C gene | 15 | 15 | 0 |
| IG D gene | 10 | 0 | 10 | |
| IG C pseudogene | 9 | 10 | 0 | |
| IG J gene | 18 | 8 | 10 | |
| IG J pseudogene | 3 | 3 | 0 | |
| IG pseudogene | 1 | 1 | 0 | |
| IG V gene | 148 | 148 | 0 | |
| IG V pseudogene | 216 | 214 | 2 | |
| TR C gene | 7 | 7 | 0 | |
| TR J gene | 80 | 73 | 7 | |
| TR J pseudogene | 4 | 4 | 0 | |
| TR V gene | 108 | 108 | 0 | |
| TR V pseudogene | 33 | 33 | 0 | |
| Unknown | StringTie | 48 | 48 | 0 |
| total | 63,494 | 63,421 | 73 |
Counts of CHM13 genes (without chrY) mapped by Liftoff to the KSA001 genome assembly.