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Arabidopsis thaliana vs Populus trichocarpa LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) 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.


Number of alignment blocks: 170,320

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

Uncovered: 82,241,839 out of 119,667,750
Covered: 37,425,911 out of 119,667,750

Uncovered: 7,617,335 out of 33,775,569
Matches: 17,852,111 out of 33,775,569
Mismatches: 7,727,402 out of 33,775,569
Insertions: 578,721 out of 33,775,569

Populus trichocarpa

Uncovered: 379,926,240 out of 434,132,815
Covered: 54,206,575 out of 434,132,815

Uncovered: 12,378,467 out of 48,383,886
Matches: 24,339,052 out of 48,383,886
Mismatches: 10,618,869 out of 48,383,886
Insertions: 1,047,498 out of 48,383,886

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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)
     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 Populus trichocarpa
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}