Human vs Tuatara LastZ results
Human (Homo sapiens, GRCh38) and Tuatara (Sphenodon punctatus, ASM311381v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 95. 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 | Tuatara |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 320,890 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,001,759,865 out of 3,096,649,726 |
Uncovered: 7,540,378 out of 35,570,071 |
| Tuatara |
Uncovered: 4,192,910,875 out of 4,272,214,985 |
Uncovered: 4,909,847 out of 25,347,208 |
Block size distribution
| Size range | All 320,890 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 865 |
4.1 kb |
|||
| 10 bp - 100 bp | 37,717 |
2.8 Mb |
14,134 |
1.1 Mb |
|
| 100 bp - 1 kb | 270,443 |
77.4 Mb |
137,516 |
47.4 Mb |
|
| 1 kb - 10 kb | 11,860 |
19.0 Mb |
18,369 |
39.9 Mb |
|
| 10 kb - 100 kb | 4 |
91.6 kb |
424 |
9.2 Mb |
|
| 100 kb - 1 Mb | 1 |
100.2 kb |
14 |
1.8 Mb |
|