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Magnaporthe poae vs Puccinia graminis LastZ results

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

Statistics over 6,864 alignment blocks

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

Uncovered: 38,087,572 out of 39,503,331
Covered: 1,415,759 out of 39,503,331

Uncovered: 13,320,242 out of 14,559,232
Matches: 771,238 out of 14,559,232
Mismatches: 437,220 out of 14,559,232
Insertions: 30,532 out of 14,559,232
Identity over aligned base-pairs: 62.2%

Puccinia graminis

Uncovered: 87,011,185 out of 88,724,376
Covered: 1,713,191 out of 88,724,376

Uncovered: 17,238,696 out of 18,687,338
Matches: 885,892 out of 18,687,338
Mismatches: 509,090 out of 18,687,338
Insertions: 53,660 out of 18,687,338
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 6,864 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
91.0 bp
10 bp - 100 bp
1,425
101.9 kb
178
13.1 kb
100 bp - 1 kb
5,227
1.5 Mb
1,731
747.4 kb
1 kb - 10 kb
196
270.1 kb
635
1.1 Mb
10 kb - 100 kb
1
12.3 kb