Human vs Lamprey LastZ results
Human (Homo sapiens, GRCh38) and Lamprey (Petromyzon marinus, Pmarinus_7.0) 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 |
| 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 | Lamprey |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} |
Statistics over 104,310 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,082,728,491 out of 3,099,750,718 |
Uncovered: 26,949,824 out of 38,571,754 |
| Lamprey |
Uncovered: 876,368,657 out of 885,550,958 |
Uncovered: 6,160,626 out of 12,541,363 |
Block size distribution
| Size range | All 104,310 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 356 |
1.5 kb |
|||
| 10 bp - 100 bp | 23,464 |
1.8 Mb |
10,563 |
814.6 kb |
|
| 100 bp - 1 kb | 79,876 |
14.7 Mb |
46,596 |
12.3 Mb |
|
| 1 kb - 10 kb | 612 |
911.5 kb |
2,520 |
4.2 Mb |
|
| 10 kb - 100 kb | 2 |
29.2 kb |
6 |
134.1 kb |
|