Human vs Three-toed box turtle LastZ results
Human (Homo sapiens, GRCh38) and Three-toed box turtle (Terrapene carolina triunguis, T_m_triunguis-2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 99. 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 | Three-toed box 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 361,656 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 2,968,589,603 out of 3,096,649,726 |
Uncovered: 6,431,919 out of 35,602,741 |
| Three-toed box turtle |
Uncovered: 2,472,943,813 out of 2,571,267,249 |
Uncovered: 8,976,881 out of 33,075,402 |
Block size distribution
| Size range | All 361,656 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 751 |
3.9 kb |
|||
| 10 bp - 100 bp | 42,717 |
3.1 Mb |
14,850 |
1.1 Mb |
|
| 100 bp - 1 kb | 302,232 |
90.9 Mb |
123,057 |
44.2 Mb |
|
| 1 kb - 10 kb | 15,305 |
26.3 Mb |
20,371 |
47.0 Mb |
|
| 10 kb - 100 kb | 649 |
13.3 Mb |
1,411 |
32.2 Mb |
|
| 100 kb - 1 Mb | 2 |
200.6 kb |
48 |
9.4 Mb |
|