Opossum vs Tasmanian devil LastZ results
Opossum (Monodelphis domestica, ASM229v1) and Tasmanian devil (Sarcophilus harrisii, mSarHar1.11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 102. Opossum 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 | Opossum | Tasmanian devil |
|---|---|---|
| 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 2,230,276 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Opossum |
Uncovered: 1,996,159,314 out of 3,600,504,728 |
Uncovered: 3,426,378 out of 35,083,223 |
| Tasmanian devil |
Uncovered: 1,540,334,646 out of 3,086,657,325 |
Uncovered: 2,552,288 out of 33,291,752 |
Block size distribution
| Size range | All 2,230,276 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 67,264 |
444.8 kb |
|||
| 10 bp - 100 bp | 232,005 |
11.4 Mb |
21,690 |
1.5 Mb |
|
| 100 bp - 1 kb | 1,349,937 |
622.5 Mb |
91,164 |
30.8 Mb |
|
| 1 kb - 10 kb | 580,291 |
1.1 Gb |
16,583 |
37.7 Mb |
|
| 10 kb - 100 kb | 775 |
11.5 Mb |
779 |
17.8 Mb |
|
| 100 kb - 1 Mb | 4 |
507.7 kb |
111 |
37.7 Mb |
|
| 1 Mb - 10 Mb | 50 |
181.1 Mb |
|||
| 10 Mb - 100 Mb | 20 |
694.7 Mb |
|||
| 100 Mb - 1 Gb | 5 |
707.3 Mb |
|||