Aedes aegypti (LVP_AGWG) vs Culex quinquefasciatus LastZ Results
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Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) and Culex quinquefasciatus (Culex quinquefasciatus, CpipJ2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release . Aedes aegypti (LVP_AGWG) was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.
Results
Number of alignment blocks: 131,495
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Aedes aegypti |
Uncovered: 1,235,300,105 out of 1,278,732,104 |
Uncovered: 3,289,624 out of 24,249,714 |
| Culex quinquefasciatus |
Uncovered: 535,442,192 out of 579,057,705 |
Uncovered: 4,053,353 out of 24,938,790 |
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | |
| 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
|
| Other parameters (other) | --ambiguous=iupac |
Chunking parameters
| Aedes aegypti (LVP_AGWG) | Culex quinquefasciatus | |
|---|---|---|
| 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} |
