Anopheles arabiensis vs Anopheles merus LastZ Results
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Anopheles arabiensis (Anopheles arabiensis, AaraD1) and Anopheles merus (Anopheles merus, AmerM2) were aligned using the LastZ alignment algorithm (LastZ) in VectorBase release 1506. Anopheles arabiensis 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: 80,030
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Anopheles arabiensis |
Uncovered: 52,272,950 out of 246,567,867 |
Uncovered: 194,389 out of 21,157,777 |
Anopheles merus |
Uncovered: 91,945,703 out of 288,048,996 |
Uncovered: 102,484 out of 19,203,252 |
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 --identity=80..100 --matchcount=1000 |
Chunking parameters
Anopheles arabiensis | Anopheles merus | |
---|---|---|
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} |