Schizosaccharomyces octosporus vs Schizosaccharomyces pombe LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 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 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 7,013 alignment blocks

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

Uncovered: 3,918,710 out of 11,634,473
Covered: 7,715,763 out of 11,634,473

Uncovered: 612,869 out of 6,921,651
Matches: 4,200,083 out of 6,921,651
Mismatches: 1,976,551 out of 6,921,651
Insertions: 132,148 out of 6,921,651
Identity over aligned base-pairs: 66.6%

Schizosaccharomyces pombe

Uncovered: 4,949,617 out of 12,631,379
Covered: 7,681,762 out of 12,631,379

Uncovered: 921,854 out of 7,176,910
Matches: 4,157,231 out of 7,176,910
Mismatches: 1,954,325 out of 7,176,910
Insertions: 143,500 out of 7,176,910
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 7,013 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14
110.0 bp
10 bp - 100 bp
640
41.0 kb
201
13.0 kb
100 bp - 1 kb
3,456
1.5 Mb
401
113.9 kb
1 kb - 10 kb
2,900
6.5 Mb
135
361.9 kb
10 kb - 100 kb
3
38.6 kb
55
2.0 Mb
100 kb - 1 Mb
20
5.7 Mb