Nasonia vitripennis vs Bombus impatiens LastZ Results

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Nasonia vitripennis (Nasonia vitripennis, Nvit_2.1) and Bombus impatiens (Bombus impatiens, BIMP_2.0) 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: 67,428

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

Uncovered: 272,085,695 out of 295,780,872
Covered: 23,695,177 out of 295,780,872

Uncovered: 11,304,697 out of 24,175,229
Matches: 8,601,988 out of 24,175,229
Mismatches: 3,932,121 out of 24,175,229
Insertions: 336,423 out of 24,175,229

Bombus impatiens

Uncovered: 226,192,723 out of 249,185,056
Covered: 22,992,333 out of 249,185,056

Uncovered: 8,055,165 out of 22,494,304
Matches: 9,640,992 out of 22,494,304
Mismatches: 4,500,611 out of 22,494,304
Insertions: 297,536 out of 22,494,304

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 impatiens
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}