Drosophila melanogaster vs Drosophila ananassae LastZ Results
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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila ananassae (Drosophila ananassae, dana_caf1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 78. Drosophila melanogaster 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: 108,898
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Drosophila melanogaster |
Uncovered: 50,596,083 out of 143,725,995 |
Uncovered: 919,309 out of 22,883,909 |
Drosophila ananassae |
Uncovered: 137,379,533 out of 230,993,012 |
Uncovered: 1,060,121 out of 22,156,670 |
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
Drosophila melanogaster | Drosophila ananassae | |
---|---|---|
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} |