Bombus terrestris vs Atta cephalotes LastZ Results
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Bombus terrestris (Bombus terrestris, Bter_1.0) and Atta cephalotes (Atta cephalotes, Attacep1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Bombus terrestris 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: 150,438
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Bombus terrestris |
Uncovered: 198,478,259 out of 248,654,244 |
Uncovered: 2,131,260 out of 18,548,448 |
Atta cephalotes |
Uncovered: 257,563,860 out of 317,690,795 |
Uncovered: 1,824,938 out of 17,986,937 |
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
Bombus terrestris | Atta cephalotes | |
---|---|---|
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} |