Nasonia vitripennis vs Atta cephalotes LastZ Results

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Nasonia vitripennis (Nasonia vitripennis, Nvit_2.1) and Atta cephalotes (Atta cephalotes, Attacep1.0) 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: 78,046

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

Uncovered: 271,354,881 out of 295,780,872
Covered: 24,425,991 out of 295,780,872

Uncovered: 11,554,000 out of 24,175,229
Matches: 8,378,192 out of 24,175,229
Mismatches: 3,911,985 out of 24,175,229
Insertions: 331,052 out of 24,175,229

Atta cephalotes

Uncovered: 288,004,391 out of 317,690,795
Covered: 29,686,404 out of 317,690,795

Uncovered: 4,670,762 out of 17,986,937
Matches: 8,904,702 out of 17,986,937
Mismatches: 4,132,152 out of 17,986,937
Insertions: 279,321 out of 17,986,937

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 Atta cephalotes
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}