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Fusarium solani vs Puccinia triticina LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) 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 solani 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 solaniPuccinia triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 10,249 alignment blocks

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

Uncovered: 49,333,685 out of 51,291,997
Covered: 1,958,312 out of 51,291,997

Uncovered: 20,894,268 out of 22,633,081
Matches: 1,080,005 out of 22,633,081
Mismatches: 612,459 out of 22,633,081
Insertions: 46,349 out of 22,633,081
Identity over aligned base-pairs: 62.1%

Puccinia triticina

Uncovered: 160,289,960 out of 162,948,716
Covered: 2,658,756 out of 162,948,716

Uncovered: 12,285,171 out of 13,973,123
Matches: 1,033,510 out of 13,973,123
Mismatches: 576,754 out of 13,973,123
Insertions: 77,688 out of 13,973,123
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 10,249 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
27
161.0 bp
10 bp - 100 bp
1,893
135.0 kb
282
20.8 kb
100 bp - 1 kb
7,966
2.5 Mb
3,175
1.4 Mb
1 kb - 10 kb
363
493.0 kb
1,042
1.7 Mb
10 kb - 100 kb
2
23.7 kb