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Schizosaccharomyces cryophilus vs Puccinia triticina - GCA_000151525.2 LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. Schizosaccharomyces cryophilus 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

ParameterSchizosaccharomyces cryophilusPuccinia triticina - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,632 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces cryophilus

Uncovered: 10,353,714 out of 11,554,764
Covered: 1,201,050 out of 11,554,764

Uncovered: 5,838,964 out of 7,004,290
Matches: 726,168 out of 7,004,290
Mismatches: 420,010 out of 7,004,290
Insertions: 19,148 out of 7,004,290
Identity over aligned base-pairs: 62.3%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,978,461 out of 135,343,689
Covered: 1,365,228 out of 135,343,689

Uncovered: 16,329,202 out of 17,522,293
Matches: 725,362 out of 17,522,293
Mismatches: 420,694 out of 17,522,293
Insertions: 47,035 out of 17,522,293
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 5,632 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
79.0 bp
10 bp - 100 bp
1,100
79.0 kb
123
9.4 kb
100 bp - 1 kb
4,368
1.3 Mb
1,480
669.2 kb
1 kb - 10 kb
149
200.9 kb
495
881.8 kb