Human vs Siamese fighting fish LastZ results
Human (Homo sapiens, GRCh38) and Siamese fighting fish (Betta splendens, fBetSpl5.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 98. 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 | Siamese fighting fish |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 242,069 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,067,071,282 out of 3,099,750,718 |
Uncovered: 18,368,965 out of 38,571,754 |
| Siamese fighting fish |
Uncovered: 409,923,371 out of 441,371,523 |
Uncovered: 17,896,893 out of 40,133,352 |
Block size distribution
| Size range | All 242,069 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 1,585 |
7.3 kb |
1 |
4.0 bp |
|
| 10 bp - 100 bp | 50,078 |
3.8 Mb |
13,007 |
984.9 kb |
|
| 100 bp - 1 kb | 188,736 |
38.1 Mb |
69,842 |
21.8 Mb |
|
| 1 kb - 10 kb | 1,661 |
2.5 Mb |
10,174 |
20.4 Mb |
|
| 10 kb - 100 kb | 8 |
150.2 kb |
80 |
1.2 Mb |
|
| 100 kb - 1 Mb | 1 |
100.2 kb |
2 |
258.4 kb |
|