Anopheles gambiae vs Anopheles sinensis LastZ Results
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Anopheles gambiae (Anopheles gambiae, AgamP4) and Anopheles sinensis (Anopheles sinensis, AsinS2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. 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: 165,905
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Anopheles gambiae |
Uncovered: 217,634,670 out of 273,109,044 |
Uncovered: 1,873,486 out of 20,801,863 |
Anopheles sinensis |
Uncovered: 322,104,667 out of 375,763,635 |
Uncovered: 1,169,273 out of 17,240,992 |
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 | Anopheles sinensis | |
---|---|---|
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} |