Human vs Australian saltwater crocodile LastZ results
Human (Homo sapiens, GRCh38) and Australian saltwater crocodile (Crocodylus porosus, CroPor_comp1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 96. 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 | Australian saltwater crocodile |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 318,757 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,002,674,701 out of 3,099,750,718 |
Uncovered: 12,120,374 out of 38,571,754 |
| Australian saltwater crocodile |
Uncovered: 1,968,637,530 out of 2,049,536,252 |
Uncovered: 4,582,645 out of 26,208,359 |
Block size distribution
| Size range | All 318,757 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 548 |
2.8 kb |
|||
| 10 bp - 100 bp | 37,899 |
2.8 Mb |
13,180 |
976.0 kb |
|
| 100 bp - 1 kb | 267,990 |
77.8 Mb |
113,366 |
39.1 Mb |
|
| 1 kb - 10 kb | 12,268 |
19.2 Mb |
16,472 |
37.7 Mb |
|
| 10 kb - 100 kb | 48 |
1.4 Mb |
707 |
16.4 Mb |
|
| 100 kb - 1 Mb | 4 |
473.8 kb |
44 |
7.6 Mb |
|