Human vs Pig-tailed macaque LastZ results
Human (Homo sapiens, GRCh38) and Pig-tailed macaque (Macaca nemestrina, Mnem_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 | Pig-tailed macaque |
|---|---|---|
| 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 760,296 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 542,276,266 out of 3,096,649,726 |
Uncovered: 262,949 out of 35,444,608 |
| Pig-tailed macaque |
Uncovered: 493,308,787 out of 2,948,703,511 |
Uncovered: 780,074 out of 34,342,625 |
Block size distribution
| Size range | All 760,296 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 15,202 |
84.8 kb |
|||
| 10 bp - 100 bp | 53,992 |
2.8 Mb |
14,308 |
841.7 kb |
|
| 100 bp - 1 kb | 207,021 |
96.1 Mb |
35,123 |
11.8 Mb |
|
| 1 kb - 10 kb | 425,804 |
1.6 Gb |
11,595 |
32.9 Mb |
|
| 10 kb - 100 kb | 58,262 |
895.5 Mb |
1,967 |
57.9 Mb |
|
| 100 kb - 1 Mb | 15 |
1.8 Mb |
234 |
75.5 Mb |
|
| 1 Mb - 10 Mb | 228 |
923.4 Mb |
|||
| 10 Mb - 100 Mb | 90 |
1.5 Gb |
|||