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Puccinia graminis vs Schizosaccharomyces octosporus LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,440 alignment blocks

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

Uncovered: 87,396,955 out of 88,724,376
Covered: 1,327,421 out of 88,724,376

Uncovered: 17,508,006 out of 18,687,338
Matches: 717,732 out of 18,687,338
Mismatches: 411,777 out of 18,687,338
Insertions: 49,823 out of 18,687,338
Identity over aligned base-pairs: 60.9%

Schizosaccharomyces octosporus

Uncovered: 10,435,538 out of 11,634,473
Covered: 1,198,935 out of 11,634,473

Uncovered: 5,767,616 out of 6,921,651
Matches: 716,992 out of 6,921,651
Mismatches: 417,616 out of 6,921,651
Insertions: 19,427 out of 6,921,651
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 5,440 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
101.0 bp
10 bp - 100 bp
1,127
80.6 kb
134
10.0 kb
100 bp - 1 kb
4,131
1.2 Mb
1,328
601.6 kb
1 kb - 10 kb
166
234.2 kb
501
901.3 kb
10 kb - 100 kb
1
11.9 kb
1
11.9 kb