Vitis vinifera vs Populus trichocarpa LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 273,966

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 408,421,153 out of 486,265,422
Covered: 77,844,269 out of 486,265,422

Uncovered: 3,260,348 out of 32,794,161
Matches: 21,431,867 out of 32,794,161
Mismatches: 7,557,876 out of 32,794,161
Insertions: 544,070 out of 32,794,161

Populus trichocarpa

Uncovered: 353,459,398 out of 434,132,815
Covered: 80,673,417 out of 434,132,815

Uncovered: 5,831,070 out of 48,383,886
Matches: 30,880,427 out of 48,383,886
Mismatches: 10,826,839 out of 48,383,886
Insertions: 845,550 out of 48,383,886

Configuration parameters

ParameterValue
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)
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

Vitis vinifera 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}