Solanum lycopersicum vs Cynara cardunculus LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 lycopersicumCynara cardunculus
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 253,671 alignment blocks

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

Uncovered: 769,921,760 out of 827,747,456
Covered: 57,825,696 out of 827,747,456

Uncovered: 8,883,490 out of 36,416,191
Matches: 18,804,957 out of 36,416,191
Mismatches: 8,081,766 out of 36,416,191
Insertions: 645,978 out of 36,416,191
Identity over aligned base-pairs: 68.3%

Cynara cardunculus

Uncovered: 660,464,217 out of 724,667,265
Covered: 64,203,048 out of 724,667,265

Uncovered: 5,291,578 out of 32,068,562
Matches: 18,432,607 out of 32,068,562
Mismatches: 7,764,969 out of 32,068,562
Insertions: 579,408 out of 32,068,562
Identity over aligned base-pairs: 68.8%

Block size distribution

Size range All 253,671 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,748
8.7 kb
10 bp - 100 bp
49,828
3.3 Mb
26,382
1.8 Mb
100 bp - 1 kb
182,866
59.9 Mb
69,718
24.0 Mb
1 kb - 10 kb
19,196
32.2 Mb
28,303
64.1 Mb
10 kb - 100 kb
32
475.1 kb
364
6.0 Mb
100 kb - 1 Mb
1
134.8 kb
1
134.8 kb