Schizosaccharomyces japonicus vs Schizosaccharomyces pombe LastZ Results

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Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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: 7,515

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

Uncovered: 6,270,703 out of 11,733,154
Covered: 5,462,451 out of 11,733,154

Uncovered: 1,936,814 out of 6,846,208
Matches: 3,120,073 out of 6,846,208
Mismatches: 1,664,283 out of 6,846,208
Insertions: 125,038 out of 6,846,208

Schizosaccharomyces pombe 972h-

Uncovered: 7,322,499 out of 12,631,379
Covered: 5,308,880 out of 12,631,379

Uncovered: 2,334,433 out of 7,176,910
Matches: 3,071,528 out of 7,176,910
Mismatches: 1,642,417 out of 7,176,910
Insertions: 128,532 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 japonicus 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}