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Puccinia graminis vs Schizosaccharomyces pombe LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Puccinia graminis 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 graminisSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,370 alignment blocks

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

Uncovered: 87,391,072 out of 88,724,376
Covered: 1,333,304 out of 88,724,376

Uncovered: 17,509,093 out of 18,687,338
Matches: 717,131 out of 18,687,338
Mismatches: 412,823 out of 18,687,338
Insertions: 48,291 out of 18,687,338
Identity over aligned base-pairs: 60.9%

Schizosaccharomyces pombe

Uncovered: 11,425,221 out of 12,631,379
Covered: 1,206,158 out of 12,631,379

Uncovered: 6,015,766 out of 7,176,702
Matches: 717,435 out of 7,176,702
Mismatches: 425,235 out of 7,176,702
Insertions: 18,266 out of 7,176,702
Identity over aligned base-pairs: 61.8%

Block size distribution

Size range All 5,370 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
76.0 bp
10 bp - 100 bp
1,096
78.9 kb
124
9.0 kb
100 bp - 1 kb
4,108
1.2 Mb
1,242
587.6 kb
1 kb - 10 kb
152
234.8 kb
500
909.3 kb
10 kb - 100 kb
1
11.5 kb
2
28.3 kb