In this section

Puccinia graminis vs Schizosaccharomyces japonicus LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,596 alignment blocks

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

Uncovered: 86,103,412 out of 88,724,376
Covered: 2,620,964 out of 88,724,376

Uncovered: 17,301,558 out of 18,687,338
Matches: 738,206 out of 18,687,338
Mismatches: 596,497 out of 18,687,338
Insertions: 51,077 out of 18,687,338
Identity over aligned base-pairs: 53.3%

Schizosaccharomyces japonicus

Uncovered: 10,095,887 out of 11,733,154
Covered: 1,637,267 out of 11,733,154

Uncovered: 5,661,251 out of 6,846,208
Matches: 744,345 out of 6,846,208
Mismatches: 420,532 out of 6,846,208
Insertions: 20,080 out of 6,846,208
Identity over aligned base-pairs: 62.8%

Block size distribution

Size range All 6,596 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
82.0 bp
10 bp - 100 bp
1,197
85.9 kb
157
11.3 kb
100 bp - 1 kb
5,094
1.6 Mb
1,879
811.5 kb
1 kb - 10 kb
276
406.0 kb
689
1.2 Mb
10 kb - 100 kb
11
649.6 kb
6
437.4 kb
100 kb - 1 Mb
3
350.2 kb
4
563.9 kb