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Magnaporthe oryzae vs Puccinia triticina LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) 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 triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 10,777 alignment blocks

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

Uncovered: 36,946,552 out of 41,027,733
Covered: 4,081,181 out of 41,027,733

Uncovered: 14,840,464 out of 16,744,523
Matches: 942,746 out of 16,744,523
Mismatches: 920,552 out of 16,744,523
Insertions: 40,761 out of 16,744,523
Identity over aligned base-pairs: 49.5%

Puccinia triticina

Uncovered: 159,893,270 out of 162,948,716
Covered: 3,055,446 out of 162,948,716

Uncovered: 12,305,989 out of 13,973,123
Matches: 1,017,129 out of 13,973,123
Mismatches: 576,007 out of 13,973,123
Insertions: 73,998 out of 13,973,123
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 10,777 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
169.0 bp
10 bp - 100 bp
2,015
140.0 kb
475
32.3 kb
100 bp - 1 kb
7,708
2.5 Mb
3,055
1.3 Mb
1 kb - 10 kb
927
1.7 Mb
1,386
2.8 Mb
10 kb - 100 kb
90
1.3 Mb
104
1.5 Mb