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Solanum lycopersicum vs Solanum tuberosum LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Solanum lycopersicum 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

ParameterSolanum lycopersicumSolanum tuberosum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 591,651 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 487,424,150 out of 827,747,456
Covered: 340,323,306 out of 827,747,456

Uncovered: 2,138,381 out of 35,932,555
Matches: 31,317,979 out of 35,932,555
Mismatches: 2,311,189 out of 35,932,555
Insertions: 165,006 out of 35,932,555
Identity over aligned base-pairs: 92.7%

Solanum tuberosum

Uncovered: 483,293,563 out of 810,654,046
Covered: 327,360,483 out of 810,654,046

Uncovered: 5,770,147 out of 36,745,425
Matches: 28,463,158 out of 36,745,425
Mismatches: 2,197,996 out of 36,745,425
Insertions: 314,124 out of 36,745,425
Identity over aligned base-pairs: 91.9%

Block size distribution

Size range All 591,651 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11,159
68.5 kb
10 bp - 100 bp
107,467
6.1 Mb
26,805
1.7 Mb
100 bp - 1 kb
332,132
136.0 Mb
62,993
22.0 Mb
1 kb - 10 kb
139,545
296.7 Mb
70,350
198.7 Mb
10 kb - 100 kb
1,331
31.4 Mb
2,830
68.4 Mb
100 kb - 1 Mb
17
1.9 Mb
74
13.9 Mb
1 Mb - 10 Mb
24
85.6 Mb
10 Mb - 100 Mb
6
81.9 Mb