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Magnaporthe poae vs Puccinia triticina LastZ results

Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) 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 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 poaePuccinia triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,196 alignment blocks

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

Uncovered: 37,894,593 out of 39,503,331
Covered: 1,608,738 out of 39,503,331

Uncovered: 13,190,029 out of 14,559,232
Matches: 854,961 out of 14,559,232
Mismatches: 475,362 out of 14,559,232
Insertions: 38,880 out of 14,559,232
Identity over aligned base-pairs: 62.4%

Puccinia triticina

Uncovered: 160,762,528 out of 162,948,716
Covered: 2,186,188 out of 162,948,716

Uncovered: 12,464,719 out of 13,973,123
Matches: 920,269 out of 13,973,123
Mismatches: 521,681 out of 13,973,123
Insertions: 66,454 out of 13,973,123
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 8,196 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
89.0 bp
10 bp - 100 bp
1,619
115.3 kb
252
18.9 kb
100 bp - 1 kb
6,300
1.9 Mb
2,375
1.0 Mb
1 kb - 10 kb
261
384.4 kb
771
1.4 Mb
10 kb - 100 kb
1
12.1 kb