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Fusarium oxysporum vs Fusarium verticillioides LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. 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 oxysporumFusarium verticillioides
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 22,928 alignment blocks

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

Uncovered: 18,614,460 out of 61,470,697
Covered: 42,856,237 out of 61,470,697

Uncovered: 2,763,774 out of 21,631,774
Matches: 16,680,883 out of 21,631,774
Mismatches: 2,092,143 out of 21,631,774
Insertions: 94,974 out of 21,631,774
Identity over aligned base-pairs: 88.4%

Fusarium verticillioides

Uncovered: 3,834,359 out of 41,885,085
Covered: 38,050,726 out of 41,885,085

Uncovered: 984,879 out of 17,841,847
Matches: 15,098,636 out of 17,841,847
Mismatches: 1,697,622 out of 17,841,847
Insertions: 60,710 out of 17,841,847
Identity over aligned base-pairs: 89.6%

Block size distribution

Size range All 22,928 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
175
1.1 kb
10 bp - 100 bp
3,513
233.0 kb
1,985
140.6 kb
100 bp - 1 kb
11,952
4.3 Mb
6,621
2.3 Mb
1 kb - 10 kb
6,161
18.7 Mb
2,874
6.0 Mb
10 kb - 100 kb
1,127
22.0 Mb
120
3.4 Mb
100 kb - 1 Mb
13
4.6 Mb
1 Mb - 10 Mb
14
28.9 Mb