Schizosaccharomyces octosporus vs Schizosaccharomyces cryophilus LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Schizosaccharomyces octosporus was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterSchizosaccharomyces octosporusSchizosaccharomyces cryophilus
Chunk size10,000,00010,000,000
Overlap00
Group set size00
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,898 alignment blocks

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

Uncovered: 1,135,216 out of 11,634,473
Covered: 10,499,257 out of 11,634,473

Uncovered: 22,868 out of 6,921,651
Matches: 5,574,152 out of 6,921,651
Mismatches: 1,292,984 out of 6,921,651
Insertions: 31,647 out of 6,921,651
Identity over aligned base-pairs: 80.8%

Schizosaccharomyces cryophilus

Uncovered: 1,305,161 out of 11,554,764
Covered: 10,249,603 out of 11,554,764

Uncovered: 193,984 out of 7,004,290
Matches: 5,508,898 out of 7,004,290
Mismatches: 1,272,241 out of 7,004,290
Insertions: 29,167 out of 7,004,290
Identity over aligned base-pairs: 80.9%

Block size distribution

Size range All 2,898 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25
133.0 bp
10 bp - 100 bp
384
22.5 kb
160
10.6 kb
100 bp - 1 kb
1,049
383.0 kb
275
92.3 kb
1 kb - 10 kb
1,078
4.2 Mb
144
331.6 kb
10 kb - 100 kb
362
6.2 Mb
6
260.8 kb
100 kb - 1 Mb
17
6.9 Mb
1 Mb - 10 Mb
3
3.3 Mb