Human vs Sooty mangabey LastZ results
Human (Homo sapiens, GRCh38) and Sooty mangabey (Cercocebus atys, Caty_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 91. 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 | Sooty mangabey |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 789,546 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 560,398,617 out of 3,096,649,726 |
Uncovered: 384,060 out of 35,444,608 |
| Sooty mangabey |
Uncovered: 407,612,281 out of 2,848,246,356 |
Uncovered: 793,346 out of 34,351,134 |
Block size distribution
| Size range | All 789,546 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 14,556 |
81.4 kb |
|||
| 10 bp - 100 bp | 84,039 |
4.2 Mb |
15,542 |
910.9 kb |
|
| 100 bp - 1 kb | 226,726 |
98.3 Mb |
35,357 |
11.4 Mb |
|
| 1 kb - 10 kb | 403,724 |
1.5 Gb |
9,833 |
28.2 Mb |
|
| 10 kb - 100 kb | 60,501 |
933.9 Mb |
2,021 |
55.3 Mb |
|
| 100 kb - 1 Mb | 236 |
77.3 Mb |
|||
| 1 Mb - 10 Mb | 273 |
1.0 Gb |
|||
| 10 Mb - 100 Mb | 83 |
1.4 Gb |
|||