Human vs Coho salmon LastZ results
Human (Homo sapiens, GRCh38) and Coho salmon (Oncorhynchus kisutch, Okis_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 101. 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 |
| 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 | Human | Coho salmon |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 416,168 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,059,110,381 out of 3,096,649,726 |
Uncovered: 13,605,601 out of 35,634,800 |
| Coho salmon |
Uncovered: 2,311,880,783 out of 2,375,894,934 |
Uncovered: 37,068,251 out of 81,688,917 |
Block size distribution
| Size range | All 416,168 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 3,475 |
15.5 kb |
|||
| 10 bp - 100 bp | 82,940 |
6.2 Mb |
27,721 |
2.1 Mb |
|
| 100 bp - 1 kb | 326,490 |
66.2 Mb |
144,314 |
42.5 Mb |
|
| 1 kb - 10 kb | 3,254 |
5.0 Mb |
15,535 |
30.3 Mb |
|
| 10 kb - 100 kb | 8 |
217.5 kb |
140 |
2.3 Mb |
|
| 100 kb - 1 Mb | 1 |
100.2 kb |
4 |
483.9 kb |
|