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Magnaporthe poae vs Schizosaccharomyces pombe LastZ results

Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,976 alignment blocks

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

Uncovered: 37,973,052 out of 39,503,331
Covered: 1,530,279 out of 39,503,331

Uncovered: 13,180,747 out of 14,559,232
Matches: 807,874 out of 14,559,232
Mismatches: 529,780 out of 14,559,232
Insertions: 40,831 out of 14,559,232
Identity over aligned base-pairs: 58.6%

Schizosaccharomyces pombe

Uncovered: 11,041,133 out of 12,631,379
Covered: 1,590,246 out of 12,631,379

Uncovered: 5,627,331 out of 7,176,702
Matches: 907,454 out of 7,176,702
Mismatches: 616,019 out of 7,176,702
Insertions: 25,898 out of 7,176,702
Identity over aligned base-pairs: 58.6%

Block size distribution

Size range All 3,976 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
49.0 bp
10 bp - 100 bp
571
40.4 kb
90
7.2 kb
100 bp - 1 kb
2,995
1.1 Mb
1,096
567.1 kb
1 kb - 10 kb
401
650.2 kb
663
1.2 Mb
10 kb - 100 kb
1
13.6 kb