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Magnaporthe oryzae vs Magnaporthe poae LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. 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 oryzaeMagnaporthe poae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 24,140 alignment blocks

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

Uncovered: 24,294,120 out of 41,027,733
Covered: 16,733,613 out of 41,027,733

Uncovered: 4,834,602 out of 16,744,523
Matches: 7,394,451 out of 16,744,523
Mismatches: 4,214,836 out of 16,744,523
Insertions: 300,634 out of 16,744,523
Identity over aligned base-pairs: 62.1%

Magnaporthe poae

Uncovered: 24,720,288 out of 39,503,331
Covered: 14,783,043 out of 39,503,331

Uncovered: 4,635,983 out of 14,559,232
Matches: 6,832,428 out of 14,559,232
Mismatches: 2,744,967 out of 14,559,232
Insertions: 345,854 out of 14,559,232
Identity over aligned base-pairs: 68.9%

Block size distribution

Size range All 24,140 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
64
397.0 bp
10 bp - 100 bp
2,522
163.5 kb
605
39.5 kb
100 bp - 1 kb
15,802
6.5 Mb
3,756
1.6 Mb
1 kb - 10 kb
5,706
11.4 Mb
3,227
8.8 Mb
10 kb - 100 kb
46
772.9 kb
368
8.1 Mb
100 kb - 1 Mb
3
396.2 kb