Arabidopsis thaliana vs Malus domestica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Malus domestica (Malus domestica, ASM211411v1) 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: 202,847

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

Uncovered: 81,326,507 out of 119,667,750
Covered: 38,341,243 out of 119,667,750

Uncovered: 7,725,784 out of 33,775,569
Matches: 17,466,408 out of 33,775,569
Mismatches: 8,003,453 out of 33,775,569
Insertions: 579,924 out of 33,775,569

Malus domestica

Uncovered: 637,888,176 out of 702,961,352
Covered: 65,073,176 out of 702,961,352

Uncovered: 10,928,147 out of 47,560,911
Matches: 24,727,186 out of 47,560,911
Mismatches: 10,865,010 out of 47,560,911
Insertions: 1,040,568 out of 47,560,911

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 Malus domestica
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options