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Fusarium solani vs Puccinia triticina - GCA_000151525.2 LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. 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 - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,608 alignment blocks

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

Uncovered: 49,389,603 out of 51,291,997
Covered: 1,902,394 out of 51,291,997

Uncovered: 20,878,226 out of 22,633,081
Matches: 1,092,923 out of 22,633,081
Mismatches: 615,293 out of 22,633,081
Insertions: 46,639 out of 22,633,081
Identity over aligned base-pairs: 62.3%

Puccinia triticina - GCA_000151525.2

Uncovered: 133,242,418 out of 135,343,689
Covered: 2,101,271 out of 135,343,689

Uncovered: 15,732,209 out of 17,522,293
Matches: 1,100,293 out of 17,522,293
Mismatches: 607,838 out of 17,522,293
Insertions: 81,953 out of 17,522,293
Identity over aligned base-pairs: 61.5%

Block size distribution

Size range All 8,608 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
22
133.0 bp
10 bp - 100 bp
1,773
127.2 kb
222
16.6 kb
100 bp - 1 kb
6,533
2.0 Mb
2,191
1.0 Mb
1 kb - 10 kb
280
387.9 kb
864
1.5 Mb
10 kb - 100 kb
1
12.5 kb