Human vs Olive baboon LastZ results
Human (Homo sapiens, GRCh38) and Olive baboon (Papio anubis, Panubis1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 105. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 5000 |
| Threshold for gapped extension (L) | 5000 |
| Threshold for alignments between gapped alignment blocks (H) | 3000 |
| Masking count (M) | 10 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | $ENSEMBL_ROOT_DIR/ensembl-compara/scripts/pipeline/primate.matrix |
Chunking parameters
| Parameter | Human | Olive baboon |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 797,928 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 548,351,840 out of 3,096,649,726 |
Uncovered: 730,616 out of 35,703,020 |
| Olive baboon |
Uncovered: 418,384,647 out of 2,869,821,163 |
Uncovered: 3,101,886 out of 36,172,917 |
Block size distribution
| Size range | All 797,928 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 16,526 |
92.6 kb |
|||
| 10 bp - 100 bp | 66,396 |
3.4 Mb |
16,921 |
992.3 kb |
|
| 100 bp - 1 kb | 222,377 |
100.3 Mb |
37,414 |
11.6 Mb |
|
| 1 kb - 10 kb | 429,454 |
1.6 Gb |
11,323 |
36.3 Mb |
|
| 10 kb - 100 kb | 63,143 |
982.6 Mb |
3,287 |
96.9 Mb |
|
| 100 kb - 1 Mb | 32 |
4.0 Mb |
593 |
142.8 Mb |
|
| 1 Mb - 10 Mb | 37 |
82.3 Mb |
|||
| 10 Mb - 100 Mb | 34 |
1.5 Gb |
|||
| 100 Mb - 1 Gb | 7 |
842.6 Mb |
|||