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Magnaporthe oryzae vs Schizosaccharomyces octosporus LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe oryzae 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

ParameterMagnaporthe oryzaeSchizosaccharomyces octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,537 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Magnaporthe oryzae

Uncovered: 39,169,122 out of 41,027,733
Covered: 1,858,611 out of 41,027,733

Uncovered: 14,961,278 out of 16,744,523
Matches: 1,051,975 out of 16,744,523
Mismatches: 666,779 out of 16,744,523
Insertions: 64,491 out of 16,744,523
Identity over aligned base-pairs: 59.0%

Schizosaccharomyces octosporus

Uncovered: 9,762,423 out of 11,634,473
Covered: 1,872,050 out of 11,634,473

Uncovered: 5,081,418 out of 6,921,651
Matches: 1,108,923 out of 6,921,651
Mismatches: 693,408 out of 6,921,651
Insertions: 37,902 out of 6,921,651
Identity over aligned base-pairs: 60.3%

Block size distribution

Size range All 4,537 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
82.0 bp
10 bp - 100 bp
618
43.1 kb
81
6.2 kb
100 bp - 1 kb
3,391
1.3 Mb
1,325
708.7 kb
1 kb - 10 kb
517
800.8 kb
800
1.4 Mb