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Puccinia triticina vs Schizosaccharomyces pombe LastZ results

Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,853 alignment blocks

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

Uncovered: 161,441,137 out of 162,948,716
Covered: 1,507,579 out of 162,948,716

Uncovered: 12,864,891 out of 13,973,123
Matches: 670,847 out of 13,973,123
Mismatches: 391,240 out of 13,973,123
Insertions: 46,145 out of 13,973,123
Identity over aligned base-pairs: 60.5%

Schizosaccharomyces pombe

Uncovered: 11,407,351 out of 12,631,379
Covered: 1,224,028 out of 12,631,379

Uncovered: 6,005,096 out of 7,176,702
Matches: 719,456 out of 7,176,702
Mismatches: 433,262 out of 7,176,702
Insertions: 18,888 out of 7,176,702
Identity over aligned base-pairs: 61.4%

Block size distribution

Size range All 5,853 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
79.0 bp
10 bp - 100 bp
1,132
81.7 kb
118
9.1 kb
100 bp - 1 kb
4,498
1.3 Mb
1,508
667.6 kb
1 kb - 10 kb
209
306.3 kb
553
996.5 kb
10 kb - 100 kb
1
20.4 kb
2
34.8 kb