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Fusarium solani vs Fusarium verticillioides LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Fusarium solani 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 solaniFusarium verticillioides
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 28,713 alignment blocks

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

Uncovered: 23,605,269 out of 51,291,997
Covered: 27,686,728 out of 51,291,997

Uncovered: 5,186,165 out of 22,633,081
Matches: 12,381,329 out of 22,633,081
Mismatches: 4,757,550 out of 22,633,081
Insertions: 308,037 out of 22,633,081
Identity over aligned base-pairs: 71.0%

Fusarium verticillioides

Uncovered: 16,982,528 out of 41,885,085
Covered: 24,902,557 out of 41,885,085

Uncovered: 2,908,510 out of 17,841,847
Matches: 10,773,393 out of 17,841,847
Mismatches: 3,926,008 out of 17,841,847
Insertions: 233,936 out of 17,841,847
Identity over aligned base-pairs: 72.1%

Block size distribution

Size range All 28,713 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
67
401.0 bp
10 bp - 100 bp
2,789
175.3 kb
683
45.3 kb
100 bp - 1 kb
15,463
6.6 Mb
4,216
2.0 Mb
1 kb - 10 kb
10,361
23.5 Mb
4,302
9.5 Mb
10 kb - 100 kb
33
409.3 kb
156
4.0 Mb
100 kb - 1 Mb
37
12.8 Mb
1 Mb - 10 Mb
1
2.4 Mb