Opossum vs Opossum LastZ results
Opossum (Monodelphis domestica, ASM229v1) and Opossum (Monodelphis domestica, ASM229v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 100. 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 (reference) | Opossum (non-reference) |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options |
Statistics over 439,532 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Opossum |
Uncovered: 1,713,277,346 out of 1,858,552,590 |
Uncovered: 4,831,526 out of 31,202,085 |