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Fusarium verticillioides vs Schizosaccharomyces cryophilus LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium verticillioides 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 verticillioidesSchizosaccharomyces cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,272 alignment blocks

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

Uncovered: 39,542,195 out of 41,885,085
Covered: 2,342,890 out of 41,885,085

Uncovered: 15,668,490 out of 17,841,847
Matches: 1,289,185 out of 17,841,847
Mismatches: 799,889 out of 17,841,847
Insertions: 84,283 out of 17,841,847
Identity over aligned base-pairs: 59.3%

Schizosaccharomyces cryophilus

Uncovered: 9,413,524 out of 11,554,764
Covered: 2,141,240 out of 11,554,764

Uncovered: 4,921,819 out of 7,004,290
Matches: 1,262,336 out of 7,004,290
Mismatches: 772,207 out of 7,004,290
Insertions: 47,928 out of 7,004,290
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 5,272 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
33.0 bp
10 bp - 100 bp
670
47.4 kb
127
9.5 kb
100 bp - 1 kb
3,866
1.5 Mb
1,577
832.9 kb
1 kb - 10 kb
728
1.1 Mb
1,066
1.8 Mb