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Schizosaccharomyces cryophilus vs Schizosaccharomyces japonicus LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,125 alignment blocks

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

Uncovered: 6,102,078 out of 11,554,764
Covered: 5,452,686 out of 11,554,764

Uncovered: 2,116,052 out of 7,004,290
Matches: 3,089,197 out of 7,004,290
Mismatches: 1,668,278 out of 7,004,290
Insertions: 130,763 out of 7,004,290
Identity over aligned base-pairs: 63.2%

Schizosaccharomyces japonicus

Uncovered: 6,260,638 out of 11,733,154
Covered: 5,472,516 out of 11,733,154

Uncovered: 1,988,245 out of 6,846,208
Matches: 3,078,777 out of 6,846,208
Mismatches: 1,651,979 out of 6,846,208
Insertions: 127,207 out of 6,846,208
Identity over aligned base-pairs: 63.4%

Block size distribution

Size range All 8,125 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
64.0 bp
10 bp - 100 bp
1,014
69.3 kb
318
23.0 kb
100 bp - 1 kb
5,042
2.1 Mb
876
287.9 kb
1 kb - 10 kb
2,057
3.7 Mb
605
2.2 Mb
10 kb - 100 kb
1
12.3 kb
173
3.2 Mb
100 kb - 1 Mb
1
141.8 kb