Oryza sativa Japonica Group vs Populus trichocarpa LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 172,508

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 341,608,549 out of 375,049,285
Covered: 33,440,736 out of 375,049,285

Uncovered: 14,278,952 out of 34,403,043
Matches: 13,008,858 out of 34,403,043
Mismatches: 6,656,466 out of 34,403,043
Insertions: 458,767 out of 34,403,043

Populus trichocarpa

Uncovered: 391,521,029 out of 434,132,815
Covered: 42,611,786 out of 434,132,815

Uncovered: 18,836,544 out of 48,383,886
Matches: 19,287,175 out of 48,383,886
Mismatches: 9,633,692 out of 48,383,886
Insertions: 626,475 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

Oryza sativa Japonica Group 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}