Medicago truncatula vs Populus trichocarpa LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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: 233,016

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 352,642,519 out of 412,800,391
Covered: 60,157,872 out of 412,800,391

Uncovered: 14,900,069 out of 50,132,764
Matches: 24,259,681 out of 50,132,764
Mismatches: 10,200,785 out of 50,132,764
Insertions: 772,229 out of 50,132,764

Populus trichocarpa

Uncovered: 365,994,379 out of 434,132,815
Covered: 68,138,436 out of 434,132,815

Uncovered: 8,583,899 out of 48,383,886
Matches: 27,539,839 out of 48,383,886
Mismatches: 11,241,713 out of 48,383,886
Insertions: 1,018,435 out of 48,383,886

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

Medicago truncatula Populus trichocarpa
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}