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Solanum lycopersicum vs Daucus carota LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) 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 lycopersicumDaucus carota
Chunk size10,100,00010,100,000
Overlap100,000100,000
Group set size10,100,00010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 234,747 alignment blocks

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

Uncovered: 768,628,757 out of 827,747,456
Covered: 59,118,699 out of 827,747,456

Uncovered: 8,069,537 out of 35,932,555
Matches: 19,157,491 out of 35,932,555
Mismatches: 8,100,909 out of 35,932,555
Insertions: 604,618 out of 35,932,555
Identity over aligned base-pairs: 68.8%

Daucus carota

Uncovered: 358,111,769 out of 421,502,825
Covered: 63,391,056 out of 421,502,825

Uncovered: 8,682,844 out of 38,118,360
Matches: 20,316,264 out of 38,118,360
Mismatches: 8,501,618 out of 38,118,360
Insertions: 617,634 out of 38,118,360
Identity over aligned base-pairs: 69.0%

Block size distribution

Size range All 234,747 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,769
8.7 kb
10 bp - 100 bp
37,444
2.5 Mb
15,484
1.1 Mb
100 bp - 1 kb
176,517
59.8 Mb
63,393
22.8 Mb
1 kb - 10 kb
18,896
31.5 Mb
26,182
62.5 Mb
10 kb - 100 kb
121
1.9 Mb
537
9.3 Mb
100 kb - 1 Mb
1
100.3 kb