Human vs Painted turtle LastZ results
Human (Homo sapiens, GRCh38) and Painted turtle (Chrysemys picta bellii, Chrysemys_picta_bellii-3.0.3) 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 | Painted turtle |
|---|---|---|
| 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 361,225 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,982,259,214 out of 3,096,649,726 |
Uncovered: 6,646,403 out of 35,570,071 |
| Painted turtle |
Uncovered: 2,269,549,185 out of 2,365,766,571 |
Uncovered: 8,351,168 out of 33,484,189 |
Block size distribution
| Size range | All 361,225 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 825 |
4.5 kb |
|||
| 10 bp - 100 bp | 41,855 |
3.1 Mb |
14,395 |
1.1 Mb |
|
| 100 bp - 1 kb | 303,168 |
90.8 Mb |
123,857 |
44.1 Mb |
|
| 1 kb - 10 kb | 15,298 |
24.0 Mb |
20,295 |
46.1 Mb |
|
| 10 kb - 100 kb | 78 |
2.1 Mb |
905 |
20.7 Mb |
|
| 100 kb - 1 Mb | 1 |
100.3 kb |
43 |
8.1 Mb |
|