Arabidopsis thaliana vs Triticum turgidum LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum turgidum (Triticum turgidum, Svevo.v1) 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: 299,840

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

Uncovered: 91,784,354 out of 119,667,750
Covered: 27,883,396 out of 119,667,750

Uncovered: 13,713,327 out of 33,775,569
Matches: 12,831,436 out of 33,775,569
Mismatches: 6,784,861 out of 33,775,569
Insertions: 445,945 out of 33,775,569

Triticum turgidum

Uncovered: 10,369,576,299 out of 10,463,058,104
Covered: 93,481,805 out of 10,463,058,104

Uncovered: 43,419,594 out of 88,577,667
Matches: 28,803,563 out of 88,577,667
Mismatches: 15,237,698 out of 88,577,667
Insertions: 1,116,812 out of 88,577,667

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 Triticum turgidum
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}