Schizosaccharomyces octosporus vs Schizosaccharomyces japonicus LastZ Results

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Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 74. Schizosaccharomyces octosporus 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: 7,475

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces octosporus yFS286

Uncovered: 6,210,213 out of 11,634,473
Covered: 5,424,260 out of 11,634,473

Uncovered: 2,047,764 out of 6,921,651
Matches: 3,081,955 out of 6,921,651
Mismatches: 1,660,484 out of 6,921,651
Insertions: 131,448 out of 6,921,651

Schizosaccharomyces japonicus yFS275

Uncovered: 6,446,944 out of 11,733,154
Covered: 5,286,210 out of 11,733,154

Uncovered: 2,103,718 out of 6,846,208
Matches: 3,000,288 out of 6,846,208
Mismatches: 1,614,588 out of 6,846,208
Insertions: 127,614 out of 6,846,208

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 octosporus Schizosaccharomyces japonicus
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}