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Magnaporthe oryzae vs Puccinia graminis LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) 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. 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 oryzaePuccinia graminis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,755 alignment blocks

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

Uncovered: 38,923,235 out of 41,027,733
Covered: 2,104,498 out of 41,027,733

Uncovered: 15,330,875 out of 16,744,523
Matches: 868,742 out of 16,744,523
Mismatches: 510,489 out of 16,744,523
Insertions: 34,417 out of 16,744,523
Identity over aligned base-pairs: 61.5%

Puccinia graminis

Uncovered: 86,550,816 out of 88,724,376
Covered: 2,173,560 out of 88,724,376

Uncovered: 17,163,908 out of 18,687,338
Matches: 937,950 out of 18,687,338
Mismatches: 526,677 out of 18,687,338
Insertions: 58,803 out of 18,687,338
Identity over aligned base-pairs: 61.6%

Block size distribution

Size range All 8,755 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
29
143.0 bp
10 bp - 100 bp
1,869
131.1 kb
457
31.0 kb
100 bp - 1 kb
6,250
1.9 Mb
2,375
1.0 Mb
1 kb - 10 kb
605
845.1 kb
981
1.8 Mb
10 kb - 100 kb
2
40.2 kb
3
52.5 kb