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Puccinia triticina vs Saccharomyces cerevisiae LastZ results

Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) 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 triticinaSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,553 alignment blocks

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

Uncovered: 161,606,512 out of 162,948,716
Covered: 1,342,204 out of 162,948,716

Uncovered: 12,986,297 out of 13,973,123
Matches: 595,890 out of 13,973,123
Mismatches: 350,364 out of 13,973,123
Insertions: 40,572 out of 13,973,123
Identity over aligned base-pairs: 60.4%

Saccharomyces cerevisiae

Uncovered: 11,016,236 out of 12,157,105
Covered: 1,140,869 out of 12,157,105

Uncovered: 7,480,142 out of 8,596,583
Matches: 681,546 out of 8,596,583
Mismatches: 413,847 out of 8,596,583
Insertions: 21,048 out of 8,596,583
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 5,553 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
70.0 bp
10 bp - 100 bp
1,117
79.7 kb
128
9.2 kb
100 bp - 1 kb
4,249
1.2 Mb
1,384
619.9 kb
1 kb - 10 kb
175
244.9 kb
532
925.6 kb
10 kb - 100 kb
1
20.4 kb
2
35.1 kb