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Puccinia graminis vs Saccharomyces cerevisiae LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) 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 graminisSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,154 alignment blocks

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

Uncovered: 87,535,197 out of 88,724,376
Covered: 1,189,179 out of 88,724,376

Uncovered: 17,617,120 out of 18,687,338
Matches: 647,473 out of 18,687,338
Mismatches: 377,921 out of 18,687,338
Insertions: 44,824 out of 18,687,338
Identity over aligned base-pairs: 60.5%

Saccharomyces cerevisiae

Uncovered: 11,026,334 out of 12,157,105
Covered: 1,130,771 out of 12,157,105

Uncovered: 7,478,561 out of 8,596,583
Matches: 693,975 out of 8,596,583
Mismatches: 401,887 out of 8,596,583
Insertions: 22,160 out of 8,596,583
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 5,154 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14
83.0 bp
10 bp - 100 bp
1,042
75.6 kb
104
7.6 kb
100 bp - 1 kb
3,941
1.1 Mb
1,248
570.2 kb
1 kb - 10 kb
157
219.6 kb
483
861.8 kb