Chinese softshell turtle vs Three-toed box turtle LastZ results
Chinese softshell turtle (Pelodiscus sinensis, PelSin_1.0) 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. Chinese softshell turtle 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 | Chinese softshell turtle | Three-toed box turtle |
|---|---|---|
| Chunk size | 10,000,000 | 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 2,369,802 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chinese softshell turtle |
Uncovered: 850,186,765 out of 2,202,483,752 |
Uncovered: 1,509,556 out of 28,389,223 |
| Three-toed box turtle |
Uncovered: 1,369,673,192 out of 2,571,267,249 |
Uncovered: 5,979,435 out of 33,075,402 |
Block size distribution
| Size range | All 2,369,802 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 49,874 |
307.9 kb |
|||
| 10 bp - 100 bp | 355,372 |
20.9 Mb |
103,543 |
6.9 Mb |
|
| 100 bp - 1 kb | 1,532,931 |
629.4 Mb |
315,987 |
113.0 Mb |
|
| 1 kb - 10 kb | 430,599 |
767.0 Mb |
71,233 |
165.0 Mb |
|
| 10 kb - 100 kb | 1,020 |
17.4 Mb |
2,326 |
58.7 Mb |
|
| 100 kb - 1 Mb | 6 |
609.5 kb |
901 |
342.9 Mb |
|
| 1 Mb - 10 Mb | 347 |
749.0 Mb |
|||