Schizosaccharomyces japonicus vs Schizosaccharomyces cryophilus LastZ results

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 94. Schizosaccharomyces japonicus 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 japonicusSchizosaccharomyces cryophilus
Chunk size10,000,00010,000,000
Overlap00
Group set size00
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 7,506 alignment blocks

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

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
Identity over aligned base-pairs: 63.4%

Schizosaccharomyces cryophilus

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
Identity over aligned base-pairs: 63.3%

Block size distribution

Size range All 7,506 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
53.0 bp
10 bp - 100 bp
826
55.8 kb
192
13.6 kb
100 bp - 1 kb
4,667
2.0 Mb
561
190.4 kb
1 kb - 10 kb
2,004
3.6 Mb
556
2.1 Mb
10 kb - 100 kb
1
12.3 kb
173
3.2 Mb
100 kb - 1 Mb
1
141.8 kb