Zebrafish vs Lyretail cichlid LastZ results
Zebrafish (Danio rerio, GRCz11) and Lyretail cichlid (Neolamprologus brichardi, NeoBri1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Zebrafish 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 | Zebrafish | Lyretail cichlid |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 322,301 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Zebrafish |
Uncovered: 1,286,247,361 out of 1,373,471,384 |
Uncovered: 9,077,649 out of 42,031,845 |
| Lyretail cichlid |
Uncovered: 778,386,517 out of 847,910,432 |
Uncovered: 5,540,409 out of 33,846,093 |
Block size distribution
| Size range | All 322,301 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,127 |
9.4 kb |
|||
| 10 bp - 100 bp | 47,786 |
3.4 Mb |
16,418 |
1.2 Mb |
|
| 100 bp - 1 kb | 259,742 |
66.4 Mb |
86,325 |
27.5 Mb |
|
| 1 kb - 10 kb | 11,987 |
25.3 Mb |
19,382 |
49.0 Mb |
|
| 10 kb - 100 kb | 659 |
12.7 Mb |
1,384 |
27.8 Mb |
|
| 100 kb - 1 Mb | 15 |
2.3 Mb |
|||