Lamprey vs Hagfish LastZ results
Lamprey (Petromyzon marinus, Pmarinus_7.0) and Hagfish (Eptatretus burgeri, Eburgeri_3.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 93. Lamprey 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 | Lamprey | Hagfish |
|---|---|---|
| Chunk size | 10,000,000 | 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 67,044 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Lamprey |
Uncovered: 869,119,258 out of 885,550,958 |
Uncovered: 5,438,701 out of 12,541,363 |
| Hagfish |
Uncovered: 2,595,594,294 out of 2,608,383,542 |
Uncovered: 17,655,237 out of 23,977,300 |
Block size distribution
| Size range | All 67,044 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 345 |
1.4 kb |
|||
| 10 bp - 100 bp | 13,202 |
1.0 Mb |
7,004 |
547.5 kb |
|
| 100 bp - 1 kb | 52,294 |
10.0 Mb |
34,815 |
8.8 Mb |
|
| 1 kb - 10 kb | 1,146 |
3.1 Mb |
1,918 |
4.6 Mb |
|
| 10 kb - 100 kb | 47 |
1.3 Mb |
60 |
1.5 Mb |
|
| 100 kb - 1 Mb | 10 |
1.2 Mb |
10 |
1.2 Mb |
|