Arabidopsis thaliana vs Populus trichocarpa LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Populus trichocarpa (Populus trichocarpa, JGI2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 100,602

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

Uncovered: 82,141,610 out of 119,667,750
Covered: 37,526,140 out of 119,667,750

Uncovered: 6,963,452 out of 33,462,323
Matches: 18,188,456 out of 33,462,323
Mismatches: 7,767,821 out of 33,462,323
Insertions: 542,594 out of 33,462,323

Populus trichocarpa

Uncovered: 386,654,417 out of 417,137,944
Covered: 30,483,527 out of 417,137,944

Uncovered: 26,432,868 out of 46,257,415
Matches: 13,580,607 out of 46,257,415
Mismatches: 5,682,786 out of 46,257,415
Insertions: 561,154 out of 46,257,415

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)