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Magnaporthe poae vs Schizosaccharomyces cryophilus LastZ results

Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe poae 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 poaeSchizosaccharomyces cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,073 alignment blocks

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

Uncovered: 37,926,199 out of 39,503,331
Covered: 1,577,132 out of 39,503,331

Uncovered: 13,157,710 out of 14,559,232
Matches: 824,361 out of 14,559,232
Mismatches: 533,309 out of 14,559,232
Insertions: 43,852 out of 14,559,232
Identity over aligned base-pairs: 58.8%

Schizosaccharomyces cryophilus

Uncovered: 9,932,637 out of 11,554,764
Covered: 1,622,127 out of 11,554,764

Uncovered: 5,435,949 out of 7,004,290
Matches: 925,348 out of 7,004,290
Mismatches: 616,025 out of 7,004,290
Insertions: 26,968 out of 7,004,290
Identity over aligned base-pairs: 59.0%

Block size distribution

Size range All 4,073 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
37.0 bp
10 bp - 100 bp
552
38.5 kb
101
7.7 kb
100 bp - 1 kb
3,100
1.1 Mb
1,192
609.1 kb
1 kb - 10 kb
414
651.9 kb
682
1.2 Mb