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Fusarium verticillioides vs Puccinia triticina LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) 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 triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,402 alignment blocks

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

Uncovered: 40,147,369 out of 41,885,085
Covered: 1,737,716 out of 41,885,085

Uncovered: 16,279,407 out of 17,841,847
Matches: 964,340 out of 17,841,847
Mismatches: 557,161 out of 17,841,847
Insertions: 40,939 out of 17,841,847
Identity over aligned base-pairs: 61.7%

Puccinia triticina

Uncovered: 160,780,467 out of 162,948,716
Covered: 2,168,249 out of 162,948,716

Uncovered: 12,437,286 out of 13,973,123
Matches: 940,971 out of 13,973,123
Mismatches: 524,591 out of 13,973,123
Insertions: 70,275 out of 13,973,123
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 8,402 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
94.0 bp
10 bp - 100 bp
1,659
119.1 kb
264
20.3 kb
100 bp - 1 kb
6,443
2.0 Mb
2,246
1.0 Mb
1 kb - 10 kb
282
401.1 kb
813
1.4 Mb
10 kb - 100 kb
4
53.4 kb