Chinese softshell turtle vs Goodes thornscrub tortoise LastZ results
Chinese softshell turtle (Pelodiscus sinensis, PelSin_1.0) and Goodes thornscrub tortoise (Gopherus evgoodei, rGopEvg1_v1.p) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 100. 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 | Goodes thornscrub tortoise |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 1,950,709 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Chinese softshell turtle |
Uncovered: 1,082,575,975 out of 2,202,483,752 |
Uncovered: 2,250,257 out of 28,389,223 |
| Goodes thornscrub tortoise |
Uncovered: 1,161,046,762 out of 2,298,547,364 |
Uncovered: 2,309,703 out of 31,217,359 |
Block size distribution
| Size range | All 1,950,709 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 41,856 |
270.8 kb |
|||
| 10 bp - 100 bp | 236,247 |
13.6 Mb |
48,230 |
3.3 Mb |
|
| 100 bp - 1 kb | 1,278,650 |
548.0 Mb |
168,053 |
59.7 Mb |
|
| 1 kb - 10 kb | 393,717 |
684.4 Mb |
33,387 |
72.3 Mb |
|
| 10 kb - 100 kb | 236 |
3.7 Mb |
1,727 |
49.5 Mb |
|
| 100 kb - 1 Mb | 3 |
385.1 kb |
845 |
322.9 Mb |
|
| 1 Mb - 10 Mb | 341 |
742.6 Mb |
|||