Human vs Sumatran orangutan LastZ results
Human (Homo sapiens, GRCh38) and Sumatran orangutan (Pongo abelii, Susie_PABv2) 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 | Sumatran orangutan |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 323,714 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 337,405,449 out of 3,096,649,726 |
Uncovered: 173,490 out of 35,703,020 |
| Sumatran orangutan |
Uncovered: 396,170,640 out of 3,065,052,215 |
Uncovered: 489,991 out of 34,106,545 |
Block size distribution
| Size range | All 323,714 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 3,846 |
21.0 kb |
|||
| 10 bp - 100 bp | 28,793 |
1.4 Mb |
9,099 |
513.4 kb |
|
| 100 bp - 1 kb | 60,774 |
25.4 Mb |
17,084 |
5.4 Mb |
|
| 1 kb - 10 kb | 133,540 |
599.8 Mb |
5,075 |
16.7 Mb |
|
| 10 kb - 100 kb | 96,378 |
2.3 Gb |
2,280 |
74.6 Mb |
|
| 100 kb - 1 Mb | 383 |
45.7 Mb |
554 |
121.8 Mb |
|
| 1 Mb - 10 Mb | 44 |
124.2 Mb |
|||
| 10 Mb - 100 Mb | 28 |
1.4 Gb |
|||
| 100 Mb - 1 Gb | 8 |
1.2 Gb |
|||