Schizosaccharomyces japonicus vs Schizosaccharomyces pombe LastZ results

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 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 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 7,515 alignment blocks

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

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
Identity over aligned base-pairs: 63.6%

Schizosaccharomyces pombe

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
Identity over aligned base-pairs: 63.4%

Block size distribution

Size range All 7,515 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
42.0 bp
10 bp - 100 bp
823
56.3 kb
175
13.1 kb
100 bp - 1 kb
4,686
2.0 Mb
495
156.6 kb
1 kb - 10 kb
1,998
3.6 Mb
551
2.1 Mb
10 kb - 100 kb
172
3.3 Mb
100 kb - 1 Mb
1
105.2 kb