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Fusarium solani vs Schizosaccharomyces japonicus LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium solani 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

ParameterFusarium solaniSchizosaccharomyces japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,834 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Fusarium solani

Uncovered: 48,637,038 out of 51,291,997
Covered: 2,654,959 out of 51,291,997

Uncovered: 20,173,816 out of 22,633,081
Matches: 1,465,159 out of 22,633,081
Mismatches: 890,281 out of 22,633,081
Insertions: 103,825 out of 22,633,081
Identity over aligned base-pairs: 59.6%

Schizosaccharomyces japonicus

Uncovered: 9,425,826 out of 11,733,154
Covered: 2,307,328 out of 11,733,154

Uncovered: 4,674,982 out of 6,846,208
Matches: 1,331,516 out of 6,846,208
Mismatches: 786,517 out of 6,846,208
Insertions: 53,193 out of 6,846,208
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 5,834 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
80.0 bp
10 bp - 100 bp
772
52.6 kb
170
11.9 kb
100 bp - 1 kb
4,188
1.7 Mb
1,673
910.0 kb
1 kb - 10 kb
861
1.4 Mb
1,233
2.2 Mb
10 kb - 100 kb
1
11.6 kb