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Ashbya gossypii vs Fusarium oxysporum LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) 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 gossypiiFusarium oxysporum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,404 alignment blocks

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

Uncovered: 8,261,433 out of 9,119,312
Covered: 857,879 out of 9,119,312

Uncovered: 6,169,735 out of 7,019,450
Matches: 514,385 out of 7,019,450
Mismatches: 309,950 out of 7,019,450
Insertions: 25,380 out of 7,019,450
Identity over aligned base-pairs: 60.5%

Fusarium oxysporum

Uncovered: 60,270,856 out of 61,470,697
Covered: 1,199,841 out of 61,470,697

Uncovered: 20,535,019 out of 21,631,774
Matches: 654,715 out of 21,631,774
Mismatches: 396,566 out of 21,631,774
Insertions: 45,474 out of 21,631,774
Identity over aligned base-pairs: 59.7%

Block size distribution

Size range All 2,404 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
7.0 bp
10 bp - 100 bp
285
20.8 kb
76
6.1 kb
100 bp - 1 kb
1,774
730.3 kb
832
456.8 kb
1 kb - 10 kb
344
528.8 kb
468
817.1 kb