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Schizosaccharomyces cryophilus vs Schizosaccharomyces pombe LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 74. Schizosaccharomyces cryophilus 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 cryophilusSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 7,089 alignment blocks

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

Uncovered: 3,725,685 out of 11,554,764
Covered: 7,829,079 out of 11,554,764

Uncovered: 634,597 out of 7,004,290
Matches: 4,254,183 out of 7,004,290
Mismatches: 1,985,465 out of 7,004,290
Insertions: 130,045 out of 7,004,290
Identity over aligned base-pairs: 66.8%

Schizosaccharomyces pombe

Uncovered: 4,884,051 out of 12,631,379
Covered: 7,747,328 out of 12,631,379

Uncovered: 880,082 out of 7,176,910
Matches: 4,198,526 out of 7,176,910
Mismatches: 1,956,508 out of 7,176,910
Insertions: 141,794 out of 7,176,910
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 7,089 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
25.0 bp
10 bp - 100 bp
656
41.4 kb
194
12.4 kb
100 bp - 1 kb
3,510
1.6 Mb
466
142.9 kb
1 kb - 10 kb
2,914
6.6 Mb
155
381.8 kb
10 kb - 100 kb
6
73.9 kb
61
2.3 Mb
100 kb - 1 Mb
21
5.4 Mb