Arabidopsis thaliana vs Ananas comosus LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ananas comosus (Ananas comosus, F153) 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: 117,011

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

Uncovered: 91,541,861 out of 119,667,750
Covered: 28,125,889 out of 119,667,750

Uncovered: 12,956,133 out of 33,775,569
Matches: 13,667,483 out of 33,775,569
Mismatches: 6,735,946 out of 33,775,569
Insertions: 416,007 out of 33,775,569

Ananas comosus

Uncovered: 288,441,420 out of 315,839,004
Covered: 27,397,584 out of 315,839,004

Uncovered: 10,247,006 out of 27,915,811
Matches: 11,530,697 out of 27,915,811
Mismatches: 5,703,399 out of 27,915,811
Insertions: 434,709 out of 27,915,811

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 Ananas comosus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options