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Puccinia triticina vs Schizosaccharomyces japonicus LastZ results

Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Puccinia triticina 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

ParameterPuccinia triticinaSchizosaccharomyces japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,018 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Puccinia triticina

Uncovered: 160,102,909 out of 162,948,716
Covered: 2,845,807 out of 162,948,716

Uncovered: 12,682,061 out of 13,973,123
Matches: 755,377 out of 13,973,123
Mismatches: 478,000 out of 13,973,123
Insertions: 57,685 out of 13,973,123
Identity over aligned base-pairs: 58.5%

Schizosaccharomyces japonicus

Uncovered: 9,914,829 out of 11,733,154
Covered: 1,818,325 out of 11,733,154

Uncovered: 5,586,592 out of 6,846,208
Matches: 764,263 out of 6,846,208
Mismatches: 472,991 out of 6,846,208
Insertions: 22,362 out of 6,846,208
Identity over aligned base-pairs: 60.7%

Block size distribution

Size range All 8,018 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
18
114.0 bp
10 bp - 100 bp
1,375
99.5 kb
234
17.1 kb
100 bp - 1 kb
6,224
2.0 Mb
2,533
1.1 Mb
1 kb - 10 kb
387
641.4 kb
882
1.6 Mb
10 kb - 100 kb
12
303.9 kb
11
249.5 kb
100 kb - 1 Mb
2
241.2 kb
3
358.5 kb