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Ashbya gossypii vs Puccinia graminis LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Ashbya gossypii 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

ParameterAshbya gossypiiPuccinia graminis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,192 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Ashbya gossypii

Uncovered: 8,664,440 out of 9,119,312
Covered: 454,872 out of 9,119,312

Uncovered: 6,568,338 out of 7,019,450
Matches: 279,063 out of 7,019,450
Mismatches: 162,749 out of 7,019,450
Insertions: 9,300 out of 7,019,450
Identity over aligned base-pairs: 61.9%

Puccinia graminis

Uncovered: 88,148,795 out of 88,724,376
Covered: 575,581 out of 88,724,376

Uncovered: 18,163,823 out of 18,687,338
Matches: 319,641 out of 18,687,338
Mismatches: 183,289 out of 18,687,338
Insertions: 20,585 out of 18,687,338
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 2,192 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
20.0 bp
10 bp - 100 bp
442
31.5 kb
54
4.1 kb
100 bp - 1 kb
1,683
484.2 kb
575
266.2 kb
1 kb - 10 kb
64
90.2 kb
190
335.6 kb