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Magnaporthe oryzae vs Schizosaccharomyces japonicus LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,946 alignment blocks

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

Uncovered: 37,867,758 out of 41,027,733
Covered: 3,159,975 out of 41,027,733

Uncovered: 14,620,870 out of 16,744,523
Matches: 1,180,707 out of 16,744,523
Mismatches: 864,121 out of 16,744,523
Insertions: 78,825 out of 16,744,523
Identity over aligned base-pairs: 55.6%

Schizosaccharomyces japonicus

Uncovered: 9,364,662 out of 11,733,154
Covered: 2,368,492 out of 11,733,154

Uncovered: 4,833,822 out of 6,846,208
Matches: 1,235,202 out of 6,846,208
Mismatches: 732,186 out of 6,846,208
Insertions: 44,998 out of 6,846,208
Identity over aligned base-pairs: 61.4%

Block size distribution

Size range All 5,946 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
75.0 bp
10 bp - 100 bp
756
51.8 kb
131
9.6 kb
100 bp - 1 kb
4,264
1.7 Mb
1,652
871.0 kb
1 kb - 10 kb
908
1.6 Mb
1,229
2.5 Mb
10 kb - 100 kb
7
261.4 kb
3
158.7 kb
100 kb - 1 Mb
1
113.9 kb