Schizosaccharomyces cryophilus vs Schizosaccharomyces pombe LastZ Results
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Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 74. Schizosaccharomyces cryophilus 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: 7,089
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Schizosaccharomyces cryophilus OY26 |
Uncovered: 3,725,685 out of 11,554,764 |
Uncovered: 634,597 out of 7,004,290 |
Schizosaccharomyces pombe 972h- |
Uncovered: 4,884,051 out of 12,631,379 |
Uncovered: 880,082 out of 7,176,910 |
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
Schizosaccharomyces cryophilus | Schizosaccharomyces pombe | |
---|---|---|
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} |