Chicken vs Three-toed box turtle LastZ results
Chicken (Gallus gallus, bGalGal1.mat.broiler.GRCg7b) and Three-toed box turtle (Terrapene carolina triunguis, T_m_triunguis-2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 107. Chicken 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 | Chicken | Three-toed box turtle |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | 10,100,000 |
| Masking options |
Statistics over 598,646 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chicken |
Uncovered: 684,433,993 out of 1,053,332,251 |
Uncovered: 4,450,699 out of 31,304,036 |
| Three-toed box turtle |
Uncovered: 2,189,356,655 out of 2,571,267,249 |
Uncovered: 9,404,670 out of 33,075,402 |
Block size distribution
| Size range | All 598,646 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 2,409 |
15.5 kb |
|||
| 10 bp - 100 bp | 39,671 |
2.4 Mb |
5,415 |
382.3 kb |
|
| 100 bp - 1 kb | 433,196 |
200.5 Mb |
23,511 |
8.4 Mb |
|
| 1 kb - 10 kb | 123,298 |
201.5 Mb |
6,110 |
14.1 Mb |
|
| 10 kb - 100 kb | 72 |
1.1 Mb |
461 |
13.1 Mb |
|
| 100 kb - 1 Mb | 146 |
54.6 Mb |
|||
| 1 Mb - 10 Mb | 75 |
215.5 Mb |
|||
| 10 Mb - 100 Mb | 7 |
99.4 Mb |
|||