Nasonia vitripennis vs Solenopsis invicta LastZ Results

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Nasonia vitripennis (Nasonia vitripennis, Nvit_2.1) and Solenopsis invicta (Solenopsis invicta, Si_gnG) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Nasonia vitripennis 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: 103,627

Genome coverage (bp) Coding exon coverage (bp)
Nasonia vitripennis

Uncovered: 264,469,662 out of 295,780,872
Covered: 31,311,210 out of 295,780,872

Uncovered: 10,698,938 out of 24,175,229
Matches: 8,794,638 out of 24,175,229
Mismatches: 4,338,101 out of 24,175,229
Insertions: 343,552 out of 24,175,229

Solenopsis invicta

Uncovered: 354,752,943 out of 396,024,718
Covered: 41,271,775 out of 396,024,718

Uncovered: 7,023,881 out of 21,684,807
Matches: 9,713,832 out of 21,684,807
Mismatches: 4,619,503 out of 21,684,807
Insertions: 327,591 out of 21,684,807

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

Nasonia vitripennis Solenopsis invicta
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}