Opossum vs Common wombat LastZ results
Opossum (Monodelphis domestica, ASM229v1) and Common wombat (Vombatus ursinus, bare-nosed_wombat_genome_assembly) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 98. 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 | Common wombat |
|---|---|---|
| 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 2,436,640 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Opossum |
Uncovered: 1,742,362,204 out of 3,600,504,728 |
Uncovered: 3,091,091 out of 35,083,223 |
| Common wombat |
Uncovered: 1,657,030,054 out of 3,486,597,218 |
Uncovered: 4,570,481 out of 33,831,805 |
Block size distribution
| Size range | All 2,436,640 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 85,556 |
554.9 kb |
|||
| 10 bp - 100 bp | 250,563 |
12.3 Mb |
27,863 |
1.9 Mb |
|
| 100 bp - 1 kb | 1,421,209 |
648.5 Mb |
107,035 |
35.6 Mb |
|
| 1 kb - 10 kb | 678,105 |
1.3 Gb |
21,102 |
52.0 Mb |
|
| 10 kb - 100 kb | 1,204 |
18.4 Mb |
1,739 |
38.6 Mb |
|
| 100 kb - 1 Mb | 3 |
381.6 kb |
239 |
83.3 Mb |
|
| 1 Mb - 10 Mb | 170 |
616.2 Mb |
|||
| 10 Mb - 100 Mb | 61 |
1.1 Gb |
|||