Anopheles gambiae vs Aedes aegypti LastZ Results
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Anopheles gambiae (Anopheles gambiae, AgamP4) and Aedes aegypti (Aedes aegypti, AaegL3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Anopheles gambiae 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: 66,525
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Anopheles gambiae |
Uncovered: 250,585,369 out of 273,109,044 |
Uncovered: 4,594,970 out of 21,237,323 |
Aedes aegypti |
Uncovered: 1,358,918,840 out of 1,383,974,186 |
Uncovered: 5,539,481 out of 22,630,251 |
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
Anopheles gambiae | Aedes aegypti | |
---|---|---|
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} |