Schizosaccharomyces octosporus vs Schizosaccharomyces japonicus LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,000,000
Overlap00
Group set size00
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 7,475 alignment blocks

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

Uncovered: 6,210,213 out of 11,634,473
Covered: 5,424,260 out of 11,634,473

Uncovered: 2,047,764 out of 6,921,651
Matches: 3,081,955 out of 6,921,651
Mismatches: 1,660,484 out of 6,921,651
Insertions: 131,448 out of 6,921,651
Identity over aligned base-pairs: 63.2%

Schizosaccharomyces japonicus

Uncovered: 6,446,944 out of 11,733,154
Covered: 5,286,210 out of 11,733,154

Uncovered: 2,103,718 out of 6,846,208
Matches: 3,000,288 out of 6,846,208
Mismatches: 1,614,588 out of 6,846,208
Insertions: 127,614 out of 6,846,208
Identity over aligned base-pairs: 63.3%

Block size distribution

Size range All 7,475 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
118.0 bp
10 bp - 100 bp
821
56.5 kb
167
12.3 kb
100 bp - 1 kb
4,637
2.0 Mb
522
176.0 kb
1 kb - 10 kb
1,999
3.6 Mb
513
2.1 Mb
10 kb - 100 kb
177
3.4 Mb