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Fusarium oxysporum vs Schizosaccharomyces japonicus LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium oxysporum 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 oxysporumSchizosaccharomyces japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,947 alignment blocks

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

Uncovered: 58,611,475 out of 61,470,697
Covered: 2,859,222 out of 61,470,697

Uncovered: 19,259,724 out of 21,631,774
Matches: 1,418,859 out of 21,631,774
Mismatches: 851,706 out of 21,631,774
Insertions: 101,485 out of 21,631,774
Identity over aligned base-pairs: 59.8%

Schizosaccharomyces japonicus

Uncovered: 9,418,705 out of 11,733,154
Covered: 2,314,449 out of 11,733,154

Uncovered: 4,663,895 out of 6,846,208
Matches: 1,334,108 out of 6,846,208
Mismatches: 793,806 out of 6,846,208
Insertions: 54,399 out of 6,846,208
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 5,947 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
51.0 bp
10 bp - 100 bp
838
58.2 kb
173
12.9 kb
100 bp - 1 kb
4,220
1.7 Mb
1,784
942.8 kb
1 kb - 10 kb
878
1.4 Mb
1,194
2.2 Mb
10 kb - 100 kb
3
76.2 kb
4
118.8 kb