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Fusarium verticillioides vs Puccinia graminis LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) 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 verticillioidesPuccinia graminis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,436 alignment blocks

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

Uncovered: 40,235,918 out of 41,885,085
Covered: 1,649,167 out of 41,885,085

Uncovered: 16,348,549 out of 17,841,847
Matches: 927,724 out of 17,841,847
Mismatches: 528,839 out of 17,841,847
Insertions: 36,735 out of 17,841,847
Identity over aligned base-pairs: 62.1%

Puccinia graminis

Uncovered: 86,856,171 out of 88,724,376
Covered: 1,868,205 out of 88,724,376

Uncovered: 17,114,910 out of 18,687,338
Matches: 962,816 out of 18,687,338
Mismatches: 541,421 out of 18,687,338
Insertions: 68,191 out of 18,687,338
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 7,436 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
17
83.0 bp
10 bp - 100 bp
1,560
110.8 kb
218
16.3 kb
100 bp - 1 kb
5,624
1.7 Mb
1,737
806.1 kb
1 kb - 10 kb
235
344.1 kb
751
1.3 Mb
10 kb - 100 kb
1
12.3 kb