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Fusarium solani vs Puccinia graminis LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) 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 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 solaniPuccinia graminis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,604 alignment blocks

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

Uncovered: 49,473,190 out of 51,291,997
Covered: 1,818,807 out of 51,291,997

Uncovered: 21,017,931 out of 22,633,081
Matches: 1,004,139 out of 22,633,081
Mismatches: 570,464 out of 22,633,081
Insertions: 40,547 out of 22,633,081
Identity over aligned base-pairs: 62.2%

Puccinia graminis

Uncovered: 86,574,146 out of 88,724,376
Covered: 2,150,230 out of 88,724,376

Uncovered: 17,048,134 out of 18,687,338
Matches: 1,004,357 out of 18,687,338
Mismatches: 563,990 out of 18,687,338
Insertions: 70,857 out of 18,687,338
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 8,604 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
63.0 bp
10 bp - 100 bp
1,691
120.8 kb
267
19.7 kb
100 bp - 1 kb
6,603
2.1 Mb
2,302
1.0 Mb
1 kb - 10 kb
300
406.1 kb
901
1.5 Mb
10 kb - 100 kb
1
12.8 kb