Nasonia vitripennis vs Bombus terrestris LastZ Results

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Nasonia vitripennis (Nasonia vitripennis, Nvit_2.1) and Bombus terrestris (Bombus terrestris, Bter_1.0) 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: 65,607

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

Uncovered: 271,894,634 out of 295,780,872
Covered: 23,886,238 out of 295,780,872

Uncovered: 11,337,475 out of 24,175,229
Matches: 8,575,093 out of 24,175,229
Mismatches: 3,923,325 out of 24,175,229
Insertions: 339,336 out of 24,175,229

Bombus terrestris

Uncovered: 225,994,749 out of 248,654,244
Covered: 22,659,495 out of 248,654,244

Uncovered: 4,697,299 out of 18,548,448
Matches: 9,295,186 out of 18,548,448
Mismatches: 4,275,201 out of 18,548,448
Insertions: 280,762 out of 18,548,448

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 Bombus terrestris
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}