Midas cichlid vs Zebrafish LastZ results
Midas cichlid (Amphilophus citrinellus, Midas_v5) and Zebrafish (Danio rerio, GRCz11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Midas cichlid 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 | Midas cichlid | Zebrafish |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 308,844 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Midas cichlid |
Uncovered: 783,537,510 out of 844,902,565 |
Uncovered: 5,694,189 out of 34,548,519 |
| Zebrafish |
Uncovered: 1,309,770,487 out of 1,373,471,384 |
Uncovered: 9,423,360 out of 42,031,845 |
Block size distribution
| Size range | All 308,844 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,896 |
8.5 kb |
|||
| 10 bp - 100 bp | 46,046 |
3.3 Mb |
14,597 |
1.1 Mb |
|
| 100 bp - 1 kb | 254,053 |
63.3 Mb |
78,465 |
24.5 Mb |
|
| 1 kb - 10 kb | 6,828 |
11.4 Mb |
15,244 |
37.3 Mb |
|
| 10 kb - 100 kb | 21 |
313.8 kb |
695 |
13.8 Mb |
|
| 100 kb - 1 Mb | 13 |
1.8 Mb |
|||