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Fusarium verticillioides vs Schizosaccharomyces octosporus LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,137 alignment blocks

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

Uncovered: 39,509,621 out of 41,885,085
Covered: 2,375,464 out of 41,885,085

Uncovered: 15,671,373 out of 17,841,847
Matches: 1,286,210 out of 17,841,847
Mismatches: 798,602 out of 17,841,847
Insertions: 85,662 out of 17,841,847
Identity over aligned base-pairs: 59.3%

Schizosaccharomyces octosporus

Uncovered: 9,497,378 out of 11,634,473
Covered: 2,137,095 out of 11,634,473

Uncovered: 4,850,430 out of 6,921,651
Matches: 1,256,099 out of 6,921,651
Mismatches: 766,916 out of 6,921,651
Insertions: 48,206 out of 6,921,651
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 5,137 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
47.0 bp
10 bp - 100 bp
680
47.5 kb
124
9.4 kb
100 bp - 1 kb
3,664
1.4 Mb
1,515
812.9 kb
1 kb - 10 kb
785
1.2 Mb
1,066
1.8 Mb
10 kb - 100 kb
3
40.9 kb