Human vs Tree Shrew LastZ results
Human (Homo sapiens, GRCh38) and Tree Shrew (Tupaia belangeri, TREESHREW) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 76. 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) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Masking count (M) | |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Human | Tree Shrew |
|---|---|---|
| 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} |
Statistics over 2,023,756 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,031,862,685 out of 3,096,649,726 |
Uncovered: 6,730,824 out of 35,228,305 |
| Tree Shrew |
Uncovered: 2,678,156,003 out of 3,670,341,392 |
Uncovered: 4,697,417 out of 24,459,053 |
Block size distribution
| Size range | All 2,023,756 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 48,822 |
318.4 kb |
|||
| 10 bp - 100 bp | 226,362 |
12.9 Mb |
23,672 |
1.6 Mb |
|
| 100 bp - 1 kb | 1,437,634 |
610.8 Mb |
126,307 |
53.9 Mb |
|
| 1 kb - 10 kb | 310,908 |
489.0 Mb |
62,882 |
165.3 Mb |
|
| 10 kb - 100 kb | 30 |
349.0 kb |
11,790 |
415.6 Mb |
|
| 100 kb - 1 Mb | 2,440 |
474.9 Mb |
|||
| 1 Mb - 10 Mb | 2 |
2.1 Mb |
|||