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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
Covered: 7,829,079 out of 11,554,764

Uncovered: 634,597 out of 7,004,290
Matches: 4,254,183 out of 7,004,290
Mismatches: 1,985,465 out of 7,004,290
Insertions: 130,045 out of 7,004,290

Schizosaccharomyces pombe 972h-

Uncovered: 4,884,051 out of 12,631,379
Covered: 7,747,328 out of 12,631,379

Uncovered: 880,082 out of 7,176,910
Matches: 4,198,526 out of 7,176,910
Mismatches: 1,956,508 out of 7,176,910
Insertions: 141,794 out of 7,176,910

Configuration parameters

ParameterValue
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}