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Fusarium oxysporum vs Schizosaccharomyces cryophilus LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) 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 cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,450 alignment blocks

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

Uncovered: 58,999,906 out of 61,470,697
Covered: 2,470,791 out of 61,470,697

Uncovered: 19,391,970 out of 21,631,774
Matches: 1,328,444 out of 21,631,774
Mismatches: 824,168 out of 21,631,774
Insertions: 87,192 out of 21,631,774
Identity over aligned base-pairs: 59.3%

Schizosaccharomyces cryophilus

Uncovered: 9,434,956 out of 11,554,764
Covered: 2,119,808 out of 11,554,764

Uncovered: 4,941,091 out of 7,004,290
Matches: 1,247,782 out of 7,004,290
Mismatches: 767,503 out of 7,004,290
Insertions: 47,914 out of 7,004,290
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,450 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
17.0 bp
10 bp - 100 bp
660
45.8 kb
112
8.4 kb
100 bp - 1 kb
4,015
1.6 Mb
1,701
898.1 kb
1 kb - 10 kb
772
1.2 Mb
1,095
1.9 Mb