Schizosaccharomyces japonicus vs Schizosaccharomyces cryophilus LastZ Results

Back to all analyses

Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 74. Schizosaccharomyces japonicus 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: 7,506

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces japonicus yFS275

Uncovered: 6,279,398 out of 11,733,154
Covered: 5,453,756 out of 11,733,154

Uncovered: 1,986,910 out of 6,846,208
Matches: 3,081,828 out of 6,846,208
Mismatches: 1,650,597 out of 6,846,208
Insertions: 126,873 out of 6,846,208

Schizosaccharomyces cryophilus OY26

Uncovered: 6,283,074 out of 11,554,764
Covered: 5,271,690 out of 11,554,764

Uncovered: 2,217,154 out of 7,004,290
Matches: 3,030,682 out of 7,004,290
Mismatches: 1,627,654 out of 7,004,290
Insertions: 128,800 out of 7,004,290

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 japonicus Schizosaccharomyces cryophilus
Chunk size 10,000,000 10,000,000
Overlap 0 0
Group set size 0 0
Masking options {default_soft_masking => 1} {default_soft_masking => 1}