Human vs Crab-eating macaque LastZ results
Human (Homo sapiens, GRCh38) and Crab-eating macaque (Macaca fascicularis, Macaca_fascicularis_6.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 103. 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) | Primate:
A C G T
90 -330 -236 -356
-330 100 -318 -236
-236 -318 100 -330
-356 -236 -330 90
|
Chunking parameters
| Parameter | Human | Crab-eating macaque |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 898,354 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 567,770,326 out of 3,096,649,726 |
Uncovered: 711,553 out of 35,671,920 |
| Crab-eating macaque |
Uncovered: 381,331,362 out of 2,906,155,132 |
Uncovered: 633,492 out of 34,070,036 |
Block size distribution
| Size range | All 898,354 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 20,522 |
113.7 kb |
|||
| 10 bp - 100 bp | 91,136 |
4.7 Mb |
29,649 |
1.8 Mb |
|
| 100 bp - 1 kb | 271,675 |
116.3 Mb |
69,435 |
21.1 Mb |
|
| 1 kb - 10 kb | 452,445 |
1.7 Gb |
14,005 |
41.5 Mb |
|
| 10 kb - 100 kb | 62,484 |
968.9 Mb |
3,689 |
115.2 Mb |
|
| 100 kb - 1 Mb | 92 |
12.0 Mb |
668 |
137.8 Mb |
|
| 1 Mb - 10 Mb | 32 |
83.2 Mb |
|||
| 10 Mb - 100 Mb | 34 |
1.5 Gb |
|||
| 100 Mb - 1 Gb | 7 |
879.1 Mb |
|||