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Puccinia graminis vs Schizosaccharomyces cryophilus LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) 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 cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,678 alignment blocks

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

Uncovered: 87,268,928 out of 88,724,376
Covered: 1,455,448 out of 88,724,376

Uncovered: 17,494,619 out of 18,687,338
Matches: 725,649 out of 18,687,338
Mismatches: 416,247 out of 18,687,338
Insertions: 50,823 out of 18,687,338
Identity over aligned base-pairs: 60.8%

Schizosaccharomyces cryophilus

Uncovered: 10,333,014 out of 11,554,764
Covered: 1,221,750 out of 11,554,764

Uncovered: 5,832,113 out of 7,004,290
Matches: 726,357 out of 7,004,290
Mismatches: 426,404 out of 7,004,290
Insertions: 19,416 out of 7,004,290
Identity over aligned base-pairs: 62.0%

Block size distribution

Size range All 5,678 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
81.0 bp
10 bp - 100 bp
1,117
80.2 kb
132
9.6 kb
100 bp - 1 kb
4,369
1.3 Mb
1,432
661.6 kb
1 kb - 10 kb
179
245.9 kb
551
983.0 kb
10 kb - 100 kb
1
11.5 kb
1
11.8 kb