Arabidopsis thaliana vs Cynara cardunculus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. Arabidopsis thaliana 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

ParameterArabidopsis thalianaCynara 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 152,051 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 86,577,325 out of 119,667,750
Covered: 33,090,425 out of 119,667,750

Uncovered: 9,821,705 out of 33,775,569
Matches: 15,894,467 out of 33,775,569
Mismatches: 7,485,635 out of 33,775,569
Insertions: 573,762 out of 33,775,569
Identity over aligned base-pairs: 66.4%

Cynara cardunculus

Uncovered: 684,675,809 out of 724,667,265
Covered: 39,991,456 out of 724,667,265

Uncovered: 8,401,983 out of 32,068,562
Matches: 15,795,030 out of 32,068,562
Mismatches: 7,274,594 out of 32,068,562
Insertions: 596,955 out of 32,068,562
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 152,051 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,242
6.7 kb
10 bp - 100 bp
25,536
1.7 Mb
7,570
525.3 kb
100 bp - 1 kb
116,195
37.9 Mb
31,364
12.1 Mb
1 kb - 10 kb
9,078
13.7 Mb
17,590
39.0 Mb
10 kb - 100 kb
137
1.8 Mb