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Fusarium verticillioides vs Schizosaccharomyces japonicus LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,483 alignment blocks

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

Uncovered: 39,394,989 out of 41,885,085
Covered: 2,490,096 out of 41,885,085

Uncovered: 15,567,113 out of 17,841,847
Matches: 1,363,074 out of 17,841,847
Mismatches: 814,398 out of 17,841,847
Insertions: 97,262 out of 17,841,847
Identity over aligned base-pairs: 59.9%

Schizosaccharomyces japonicus

Uncovered: 9,435,587 out of 11,733,154
Covered: 2,297,567 out of 11,733,154

Uncovered: 4,652,203 out of 6,846,208
Matches: 1,349,514 out of 6,846,208
Mismatches: 790,439 out of 6,846,208
Insertions: 54,052 out of 6,846,208
Identity over aligned base-pairs: 61.5%

Block size distribution

Size range All 5,483 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
59.0 bp
10 bp - 100 bp
751
51.4 kb
132
9.3 kb
100 bp - 1 kb
3,923
1.6 Mb
1,645
875.2 kb
1 kb - 10 kb
800
1.3 Mb
1,119
2.0 Mb
10 kb - 100 kb
2
35.8 kb