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Fusarium oxysporum vs Puccinia graminis LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) 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 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 oxysporumPuccinia graminis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,510 alignment blocks

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

Uncovered: 59,509,227 out of 61,470,697
Covered: 1,961,470 out of 61,470,697

Uncovered: 20,118,068 out of 21,631,774
Matches: 941,243 out of 21,631,774
Mismatches: 534,911 out of 21,631,774
Insertions: 37,552 out of 21,631,774
Identity over aligned base-pairs: 62.2%

Puccinia graminis

Uncovered: 86,704,369 out of 88,724,376
Covered: 2,020,007 out of 88,724,376

Uncovered: 17,122,117 out of 18,687,338
Matches: 957,027 out of 18,687,338
Mismatches: 541,831 out of 18,687,338
Insertions: 66,363 out of 18,687,338
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 8,510 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
21
90.0 bp
10 bp - 100 bp
1,728
122.9 kb
272
19.8 kb
100 bp - 1 kb
6,398
2.0 Mb
2,171
951.0 kb
1 kb - 10 kb
363
540.9 kb
944
1.7 Mb
10 kb - 100 kb
1
12.0 kb