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Fusarium oxysporum vs Puccinia triticina LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium oxysporum 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

ParameterFusarium oxysporumPuccinia triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 10,085 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Fusarium oxysporum

Uncovered: 59,059,313 out of 61,470,697
Covered: 2,411,384 out of 61,470,697

Uncovered: 19,995,469 out of 21,631,774
Matches: 996,910 out of 21,631,774
Mismatches: 597,110 out of 21,631,774
Insertions: 42,285 out of 21,631,774
Identity over aligned base-pairs: 60.9%

Puccinia triticina

Uncovered: 160,265,120 out of 162,948,716
Covered: 2,683,596 out of 162,948,716

Uncovered: 12,371,916 out of 13,973,123
Matches: 973,114 out of 13,973,123
Mismatches: 554,716 out of 13,973,123
Insertions: 73,377 out of 13,973,123
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 10,085 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
93.0 bp
10 bp - 100 bp
1,965
137.4 kb
357
25.6 kb
100 bp - 1 kb
7,589
2.4 Mb
2,825
1.2 Mb
1 kb - 10 kb
506
844.4 kb
1,139
2.1 Mb
10 kb - 100 kb
9
193.2 kb
11
304.0 kb