Arabidopsis thaliana vs Cynara cardunculus LastZ Results

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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 . Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 152,051

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

Cynara cardunculus var. scolymus

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

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Cynara cardunculus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}