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Puccinia triticina vs Schizosaccharomyces octosporus LastZ results

Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Puccinia triticina 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 triticinaSchizosaccharomyces octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,906 alignment blocks

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

Uncovered: 161,469,109 out of 162,948,716
Covered: 1,479,607 out of 162,948,716

Uncovered: 12,882,176 out of 13,973,123
Matches: 662,659 out of 13,973,123
Mismatches: 382,857 out of 13,973,123
Insertions: 45,431 out of 13,973,123
Identity over aligned base-pairs: 60.7%

Schizosaccharomyces octosporus

Uncovered: 10,412,521 out of 11,634,473
Covered: 1,221,952 out of 11,634,473

Uncovered: 5,765,865 out of 6,921,651
Matches: 712,744 out of 6,921,651
Mismatches: 424,140 out of 6,921,651
Insertions: 18,902 out of 6,921,651
Identity over aligned base-pairs: 61.7%

Block size distribution

Size range All 5,906 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
92.0 bp
10 bp - 100 bp
1,188
86.6 kb
145
10.8 kb
100 bp - 1 kb
4,522
1.3 Mb
1,528
661.3 kb
1 kb - 10 kb
180
263.4 kb
544
962.2 kb
10 kb - 100 kb
1
20.4 kb
3
47.6 kb